Starting phenix.real_space_refine on Thu May 15 09:49:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.map" model { file = "/net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox1_17252/05_2025/8ox1_17252.cif" } resolution = 2.7 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= 0.001 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 293 5.49 5 S 18 5.16 5 C 7423 2.51 5 N 2502 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13258 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 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: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 511 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "M" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 575 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.78, per 1000 atoms: 0.66 Number of scatterers: 13258 At special positions: 0 Unit cell: (101.598, 117.292, 128.03, 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 18 16.00 P 293 15.00 O 3022 8.00 N 2502 7.00 C 7423 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: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 69.5% alpha, 2.7% beta 140 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.552A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.521A 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 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.614A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 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 'C' and resid 112 through 116 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 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.524A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.367A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 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 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'L' and resid 385 through 398 removed outlier: 3.761A pdb=" N LEU L 391 " --> pdb=" O GLU L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 410 Processing helix chain 'L' and resid 416 through 431 Processing helix chain 'M' and resid 384 through 398 Processing helix chain 'M' and resid 402 through 410 Processing helix chain 'M' and resid 416 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.068A 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 96 through 98 removed outlier: 6.738A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.099A 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: 6.685A 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 83 through 84 removed outlier: 6.919A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.279A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 462 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1672 1.32 - 1.45: 5160 1.45 - 1.57: 6628 1.57 - 1.69: 582 1.69 - 1.82: 32 Bond restraints: 14074 Sorted by residual: bond pdb=" CA LYS L 411 " pdb=" CB LYS L 411 " ideal model delta sigma weight residual 1.525 1.438 0.087 1.29e-02 6.01e+03 4.58e+01 bond pdb=" O2P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.498 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.11e+01 bond pdb=" CA GLU L 386 " pdb=" CB GLU L 386 " ideal model delta sigma weight residual 1.530 1.444 0.086 1.56e-02 4.11e+03 3.04e+01 bond pdb=" O3P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 14069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 19160 2.22 - 4.45: 998 4.45 - 6.67: 51 6.67 - 8.89: 4 8.89 - 11.12: 2 Bond angle restraints: 20215 Sorted by residual: angle pdb=" C GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 110.79 117.70 -6.91 1.66e+00 3.63e-01 1.73e+01 angle pdb=" O3' DC I -58 " pdb=" C3' DC I -58 " pdb=" C2' DC I -58 " ideal model delta sigma weight residual 111.50 117.72 -6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" N LEU M 391 " pdb=" CA LEU M 391 " pdb=" C LEU M 391 " ideal model delta sigma weight residual 111.07 106.75 4.32 1.07e+00 8.73e-01 1.63e+01 angle pdb=" N GLU L 386 " pdb=" CA GLU L 386 " pdb=" C GLU L 386 " ideal model delta sigma weight residual 111.11 115.85 -4.74 1.20e+00 6.94e-01 1.56e+01 angle pdb=" N SER H 120 " pdb=" CA SER H 120 " pdb=" C SER H 120 " ideal model delta sigma weight residual 111.07 115.11 -4.04 1.07e+00 8.73e-01 1.43e+01 ... (remaining 20210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.35: 6328 33.35 - 66.69: 1450 66.69 - 100.04: 11 100.04 - 133.39: 0 133.39 - 166.74: 2 Dihedral angle restraints: 7791 sinusoidal: 5168 harmonic: 2623 Sorted by residual: dihedral pdb=" C GLU M 386 " pdb=" N GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta harmonic sigma weight residual -122.60 -133.69 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C4' DT I 35 " pdb=" C3' DT I 35 " pdb=" O3' DT I 35 " pdb=" P DA I 36 " ideal model delta sinusoidal sigma weight residual 220.00 53.26 166.74 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" O3' DA I 49 " pdb=" P DC I 50 " ideal model delta sinusoidal sigma weight residual 220.00 81.40 138.60 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2087 0.102 - 0.204: 169 0.204 - 0.306: 8 0.306 - 0.409: 2 0.409 - 0.511: 1 Chirality restraints: 2267 Sorted by residual: chirality pdb=" CA GLU M 386 " pdb=" N GLU M 386 " pdb=" C GLU M 386 " pdb=" CB GLU M 386 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" CA GLU L 386 " pdb=" N GLU L 386 " pdb=" C GLU L 386 " pdb=" CB GLU L 386 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA LYS L 429 " pdb=" N LYS L 429 " pdb=" C LYS L 429 " pdb=" CB LYS L 429 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2264 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -21 " 0.046 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG J -21 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -21 " -0.018 2.00e-02 2.50e+03 pdb=" N7 DG J -21 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DG J -21 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG J -21 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG J -21 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG J -21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J -21 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG J -21 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DG J -21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J -21 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " -0.043 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" N1 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " -0.027 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -35 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.30e+00 pdb=" N9 DA J -35 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DA J -35 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J -35 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA J -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA J -35 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA J -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA J -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA J -35 " -0.012 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3474 2.84 - 3.36: 11613 3.36 - 3.87: 26368 3.87 - 4.39: 30725 4.39 - 4.90: 42295 Nonbonded interactions: 114475 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DG J 70 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU M 387 " pdb=" N ASN M 413 " model vdw 2.336 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.349 3.040 nonbonded pdb=" O ARG L 380 " pdb=" NE2 GLN L 381 " model vdw 2.403 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.418 3.040 ... (remaining 114470 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 25 through 122) } ncs_group { reference = (chain 'L' and resid 377 through 433) selection = (chain 'M' and resid 377 through 433) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 4.020 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.560 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.009 0.112 14074 Z= 0.516 Angle : 1.054 11.117 20215 Z= 0.678 Chirality : 0.063 0.511 2267 Planarity : 0.006 0.045 1542 Dihedral : 25.999 166.737 6097 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 879 helix: 1.24 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP M 385 HIS 0.008 0.002 HIS D 46 PHE 0.020 0.005 PHE A 104 TYR 0.028 0.005 TYR G 50 ARG 0.039 0.002 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.14424 ( 812) hydrogen bonds : angle 4.51158 ( 2065) covalent geometry : bond 0.00862 (14074) covalent geometry : angle 1.05379 (20215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8853 (mtt) cc_final: 0.8648 (mtp) REVERT: B 95 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7915 (mtp85) REVERT: C 36 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8905 (mmtt) REVERT: D 30 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6942 (mtp180) REVERT: D 39 TYR cc_start: 0.8633 (t80) cc_final: 0.8384 (t80) REVERT: D 96 ARG cc_start: 0.8831 (mtt-85) cc_final: 0.8505 (mtt-85) REVERT: E 56 LYS cc_start: 0.9195 (tttm) cc_final: 0.8801 (ttmt) REVERT: E 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8224 (pm20) REVERT: E 64 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8439 (mtmt) REVERT: G 11 ARG cc_start: 0.6623 (mtp-110) cc_final: 0.6320 (mtp180) REVERT: H 119 THR cc_start: 0.9121 (m) cc_final: 0.8911 (m) REVERT: L 380 ARG cc_start: 0.4563 (mmt90) cc_final: 0.4314 (ttm170) REVERT: L 406 ILE cc_start: 0.5969 (mt) cc_final: 0.5767 (tp) REVERT: L 423 ARG cc_start: 0.7788 (tpt170) cc_final: 0.7331 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 1.9083 time to fit residues: 361.1993 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067450 restraints weight = 25640.555| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.49 r_work: 0.2904 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14074 Z= 0.170 Angle : 0.561 8.874 20215 Z= 0.336 Chirality : 0.033 0.133 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.915 165.583 4236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.57 % Allowed : 8.66 % Favored : 89.76 % 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: 2.36 (0.27), residues: 879 helix: 2.38 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -0.52 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.018 0.001 PHE A 104 TYR 0.013 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 812) hydrogen bonds : angle 2.98218 ( 2065) covalent geometry : bond 0.00370 (14074) covalent geometry : angle 0.56113 (20215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8788 (tttm) cc_final: 0.8505 (ttpp) REVERT: D 30 ARG cc_start: 0.7371 (mmt90) cc_final: 0.7117 (mtp180) REVERT: D 31 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7812 (mmmm) REVERT: D 96 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8401 (mtt-85) REVERT: E 56 LYS cc_start: 0.9174 (tttm) cc_final: 0.8860 (ttmt) REVERT: E 64 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8593 (mtmt) REVERT: E 120 MET cc_start: 0.8502 (mtp) cc_final: 0.8273 (mtt) REVERT: F 22 LEU cc_start: 0.7870 (mt) cc_final: 0.7426 (mp) REVERT: G 15 LYS cc_start: 0.8837 (ttpp) cc_final: 0.8274 (tttp) REVERT: L 423 ARG cc_start: 0.7830 (tpt170) cc_final: 0.7205 (tpm170) REVERT: L 427 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7087 (mpt) REVERT: M 431 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: M 432 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (mp) outliers start: 12 outliers final: 2 residues processed: 159 average time/residue: 1.6795 time to fit residues: 284.6801 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 432 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN M 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067941 restraints weight = 25886.785| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.48 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14074 Z= 0.164 Angle : 0.534 7.048 20215 Z= 0.320 Chirality : 0.033 0.139 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.898 166.430 4236 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.84 % Allowed : 10.24 % Favored : 87.93 % 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: 2.82 (0.27), residues: 879 helix: 2.65 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 104 TYR 0.013 0.001 TYR D 37 ARG 0.006 0.000 ARG M 396 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 812) hydrogen bonds : angle 2.83409 ( 2065) covalent geometry : bond 0.00358 (14074) covalent geometry : angle 0.53381 (20215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8563 (tpt90) cc_final: 0.8288 (tpt-90) REVERT: D 30 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7125 (mtp180) REVERT: D 31 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7817 (mmmm) REVERT: D 96 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8404 (mtt-85) REVERT: E 38 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8369 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9135 (tttm) cc_final: 0.8887 (ttmp) REVERT: E 59 GLU cc_start: 0.8566 (pm20) cc_final: 0.8214 (pm20) REVERT: E 64 LYS cc_start: 0.9038 (mmtp) cc_final: 0.8585 (mtmt) REVERT: F 22 LEU cc_start: 0.7816 (mt) cc_final: 0.7383 (mp) REVERT: G 15 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8243 (tttp) REVERT: L 423 ARG cc_start: 0.7866 (tpt170) cc_final: 0.7480 (tpm170) REVERT: M 431 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8397 (mtmm) outliers start: 14 outliers final: 3 residues processed: 152 average time/residue: 1.7833 time to fit residues: 288.0402 Evaluate side-chains 135 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066367 restraints weight = 25742.523| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.50 r_work: 0.2880 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14074 Z= 0.206 Angle : 0.553 7.205 20215 Z= 0.329 Chirality : 0.034 0.142 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.009 169.264 4236 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 11.15 % Favored : 86.88 % 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: 2.86 (0.27), residues: 879 helix: 2.65 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.05 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.012 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 812) hydrogen bonds : angle 2.87234 ( 2065) covalent geometry : bond 0.00465 (14074) covalent geometry : angle 0.55335 (20215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8563 (tpt90) cc_final: 0.8322 (tpt-90) REVERT: C 73 ASN cc_start: 0.8365 (t160) cc_final: 0.8135 (t160) REVERT: D 31 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7819 (mmmm) REVERT: E 38 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8593 (pm20) cc_final: 0.8214 (pm20) REVERT: E 64 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8611 (mtmt) REVERT: F 22 LEU cc_start: 0.7902 (mt) cc_final: 0.7483 (mp) REVERT: G 15 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8220 (tttp) outliers start: 15 outliers final: 5 residues processed: 145 average time/residue: 1.7674 time to fit residues: 272.6043 Evaluate side-chains 137 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain M residue 381 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067208 restraints weight = 25833.511| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.47 r_work: 0.2903 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14074 Z= 0.157 Angle : 0.539 9.225 20215 Z= 0.322 Chirality : 0.033 0.143 2267 Planarity : 0.004 0.044 1542 Dihedral : 29.975 169.292 4236 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.23 % Allowed : 11.81 % Favored : 85.96 % 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: 2.93 (0.27), residues: 879 helix: 2.68 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.04 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 424 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 812) hydrogen bonds : angle 2.84590 ( 2065) covalent geometry : bond 0.00339 (14074) covalent geometry : angle 0.53862 (20215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8532 (tpt90) cc_final: 0.8314 (tpt-90) REVERT: C 73 ASN cc_start: 0.8337 (t0) cc_final: 0.8088 (t160) REVERT: D 31 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7810 (mmmm) REVERT: D 96 ARG cc_start: 0.8720 (mtt-85) cc_final: 0.8403 (mtt-85) REVERT: E 38 PRO cc_start: 0.8567 (Cg_exo) cc_final: 0.8341 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8591 (pm20) cc_final: 0.8259 (pm20) REVERT: E 64 LYS cc_start: 0.9060 (mmtp) cc_final: 0.8603 (mtmt) REVERT: F 22 LEU cc_start: 0.7896 (mt) cc_final: 0.7451 (mp) REVERT: G 15 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8169 (tttp) REVERT: L 423 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7590 (tpm170) REVERT: L 432 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7271 (tt) REVERT: M 431 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8420 (mtmm) outliers start: 17 outliers final: 5 residues processed: 145 average time/residue: 1.7238 time to fit residues: 266.0627 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 111 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067628 restraints weight = 25980.189| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.50 r_work: 0.2916 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14074 Z= 0.156 Angle : 0.531 9.786 20215 Z= 0.317 Chirality : 0.032 0.141 2267 Planarity : 0.004 0.046 1542 Dihedral : 29.870 169.530 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.57 % Allowed : 12.73 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.27), residues: 879 helix: 2.77 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.07 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.010 0.000 ARG L 423 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 812) hydrogen bonds : angle 2.78928 ( 2065) covalent geometry : bond 0.00337 (14074) covalent geometry : angle 0.53095 (20215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.041 Fit side-chains REVERT: A 129 ARG cc_start: 0.8538 (tpt90) cc_final: 0.8308 (tpt-90) REVERT: C 73 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8004 (t160) REVERT: D 31 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7825 (mmmm) REVERT: E 38 PRO cc_start: 0.8539 (Cg_exo) cc_final: 0.8312 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8604 (pm20) cc_final: 0.8267 (pm20) REVERT: E 64 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8594 (mtmt) REVERT: F 22 LEU cc_start: 0.7897 (mt) cc_final: 0.7438 (mp) REVERT: G 15 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8112 (tttp) REVERT: L 423 ARG cc_start: 0.8097 (tpt170) cc_final: 0.7815 (tpp-160) REVERT: L 432 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7285 (tt) REVERT: M 431 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8391 (mtmm) outliers start: 12 outliers final: 5 residues processed: 143 average time/residue: 1.7257 time to fit residues: 262.3961 Evaluate side-chains 140 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065531 restraints weight = 25955.986| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.49 r_work: 0.2859 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 14074 Z= 0.247 Angle : 0.580 9.210 20215 Z= 0.340 Chirality : 0.036 0.146 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.108 172.519 4236 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.57 % Allowed : 13.25 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.27), residues: 879 helix: 2.58 (0.20), residues: 626 sheet: None (None), residues: 0 loop : 0.05 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE E 78 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 812) hydrogen bonds : angle 2.94798 ( 2065) covalent geometry : bond 0.00561 (14074) covalent geometry : angle 0.57978 (20215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.985 Fit side-chains REVERT: A 56 LYS cc_start: 0.8922 (tttm) cc_final: 0.8562 (ttpp) REVERT: A 64 LYS cc_start: 0.8891 (mttp) cc_final: 0.8459 (mtpp) REVERT: A 129 ARG cc_start: 0.8557 (tpt90) cc_final: 0.8302 (tpt-90) REVERT: C 73 ASN cc_start: 0.8378 (t0) cc_final: 0.8044 (t160) REVERT: D 31 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7874 (mmmm) REVERT: E 38 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.8272 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8628 (pm20) cc_final: 0.8278 (pm20) REVERT: E 64 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8621 (mtmt) REVERT: F 22 LEU cc_start: 0.7900 (mt) cc_final: 0.7493 (mp) REVERT: L 422 ASP cc_start: 0.8174 (m-30) cc_final: 0.7913 (m-30) REVERT: L 423 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7832 (tpp-160) REVERT: L 432 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7336 (tt) REVERT: M 431 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8379 (mtmm) outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 1.7431 time to fit residues: 276.0343 Evaluate side-chains 146 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066906 restraints weight = 26041.076| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.49 r_work: 0.2897 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14074 Z= 0.147 Angle : 0.548 10.768 20215 Z= 0.326 Chirality : 0.033 0.150 2267 Planarity : 0.004 0.044 1542 Dihedral : 30.038 172.696 4236 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.57 % Allowed : 14.44 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.27), residues: 879 helix: 2.67 (0.20), residues: 627 sheet: None (None), residues: 0 loop : 0.10 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.005 0.001 PHE B 61 TYR 0.011 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 812) hydrogen bonds : angle 2.87106 ( 2065) covalent geometry : bond 0.00314 (14074) covalent geometry : angle 0.54781 (20215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.944 Fit side-chains REVERT: A 56 LYS cc_start: 0.8890 (tttm) cc_final: 0.8542 (ttpp) REVERT: A 129 ARG cc_start: 0.8526 (tpt90) cc_final: 0.8296 (tpt-90) REVERT: C 73 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8015 (t160) REVERT: D 31 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7752 (mmmm) REVERT: E 38 PRO cc_start: 0.8487 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8624 (pm20) cc_final: 0.8274 (pm20) REVERT: E 64 LYS cc_start: 0.9065 (mmtp) cc_final: 0.8606 (mtmt) REVERT: F 22 LEU cc_start: 0.7873 (mt) cc_final: 0.7446 (mp) REVERT: G 15 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8047 (tttp) REVERT: L 422 ASP cc_start: 0.8165 (m-30) cc_final: 0.7885 (m-30) REVERT: L 423 ARG cc_start: 0.8093 (tpt170) cc_final: 0.7851 (tpp-160) REVERT: L 432 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7349 (tt) outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 1.6465 time to fit residues: 253.1073 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.066313 restraints weight = 25831.032| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.48 r_work: 0.2884 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14074 Z= 0.215 Angle : 0.562 10.274 20215 Z= 0.331 Chirality : 0.035 0.144 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.004 175.616 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 15.22 % Favored : 83.60 % 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: 2.90 (0.27), residues: 879 helix: 2.64 (0.20), residues: 627 sheet: None (None), residues: 0 loop : 0.05 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 812) hydrogen bonds : angle 2.89682 ( 2065) covalent geometry : bond 0.00488 (14074) covalent geometry : angle 0.56239 (20215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.965 Fit side-chains REVERT: A 56 LYS cc_start: 0.8892 (tttm) cc_final: 0.8536 (ttpp) REVERT: A 64 LYS cc_start: 0.8875 (mttp) cc_final: 0.8412 (mtpt) REVERT: A 129 ARG cc_start: 0.8514 (tpt90) cc_final: 0.8266 (tpt-90) REVERT: C 73 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8081 (t160) REVERT: D 31 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7747 (mmmm) REVERT: E 38 PRO cc_start: 0.8485 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9118 (tttt) cc_final: 0.8908 (ttmp) REVERT: E 59 GLU cc_start: 0.8641 (pm20) cc_final: 0.8279 (pm20) REVERT: E 64 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8608 (mtmt) REVERT: F 22 LEU cc_start: 0.7836 (mt) cc_final: 0.7408 (mp) REVERT: G 15 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8055 (tttp) REVERT: L 406 ILE cc_start: 0.6413 (mt) cc_final: 0.6011 (tp) REVERT: L 422 ASP cc_start: 0.8206 (m-30) cc_final: 0.7923 (m-30) REVERT: L 423 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7880 (tpp-160) REVERT: L 432 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (tt) outliers start: 9 outliers final: 5 residues processed: 143 average time/residue: 1.7338 time to fit residues: 264.0068 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066683 restraints weight = 25643.209| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.47 r_work: 0.2888 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14074 Z= 0.180 Angle : 0.556 10.659 20215 Z= 0.328 Chirality : 0.033 0.145 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.003 175.631 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.18 % Allowed : 15.49 % Favored : 83.33 % 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: 2.95 (0.27), residues: 879 helix: 2.68 (0.20), residues: 627 sheet: None (None), residues: 0 loop : 0.07 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 812) hydrogen bonds : angle 2.89918 ( 2065) covalent geometry : bond 0.00399 (14074) covalent geometry : angle 0.55625 (20215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.095 Fit side-chains REVERT: A 56 LYS cc_start: 0.8887 (tttm) cc_final: 0.8569 (ttpp) REVERT: A 129 ARG cc_start: 0.8516 (tpt90) cc_final: 0.8268 (tpt-90) REVERT: C 73 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8067 (t160) REVERT: D 31 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7714 (mmmm) REVERT: E 38 PRO cc_start: 0.8482 (Cg_exo) cc_final: 0.8259 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9116 (tttt) cc_final: 0.8906 (ttmp) REVERT: E 59 GLU cc_start: 0.8638 (pm20) cc_final: 0.8274 (pm20) REVERT: E 64 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8604 (mtmt) REVERT: F 22 LEU cc_start: 0.7818 (mt) cc_final: 0.7393 (mp) REVERT: G 15 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8035 (tttp) REVERT: L 406 ILE cc_start: 0.6376 (mt) cc_final: 0.5978 (tp) REVERT: L 422 ASP cc_start: 0.8207 (m-30) cc_final: 0.7922 (m-30) REVERT: L 423 ARG cc_start: 0.8097 (tpt170) cc_final: 0.7864 (tpp-160) REVERT: L 432 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7291 (tt) outliers start: 9 outliers final: 4 residues processed: 141 average time/residue: 1.7225 time to fit residues: 259.3422 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain L residue 432 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066453 restraints weight = 25903.245| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.50 r_work: 0.2889 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14074 Z= 0.192 Angle : 0.559 10.748 20215 Z= 0.329 Chirality : 0.034 0.146 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.988 175.871 4236 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.31 % Allowed : 15.49 % Favored : 83.20 % 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: 2.93 (0.27), residues: 879 helix: 2.66 (0.20), residues: 627 sheet: None (None), residues: 0 loop : 0.06 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.010 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 812) hydrogen bonds : angle 2.89032 ( 2065) covalent geometry : bond 0.00430 (14074) covalent geometry : angle 0.55873 (20215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11186.27 seconds wall clock time: 192 minutes 30.68 seconds (11550.68 seconds total)