Starting phenix.real_space_refine on Thu Jul 31 02:12:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ox1_17252/07_2025/8ox1_17252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox1_17252/07_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_17252/07_2025/8ox1_17252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox1_17252/07_2025/8ox1_17252.map" model { file = "/net/cci-nas-00/data/ceres_data/8ox1_17252/07_2025/8ox1_17252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox1_17252/07_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-5711/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: 8.54, per 1000 atoms: 0.64 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: 3.10 Conformation dependent library (CDL) restraints added in 1.0 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: 6.21 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: 5.21 Time building geometry restraints manager: 3.50 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: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.070 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- 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 : 0.996 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: 1.9475 time to fit residues: 368.6341 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 : 0.989 ------------------------------------------------------------------------------- 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 = 41)----------------| | 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: 0.2773 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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 : 1.093 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8787 (tttm) cc_final: 0.8505 (ttpp) REVERT: D 30 ARG cc_start: 0.7368 (mmt90) cc_final: 0.7118 (mtp180) REVERT: D 31 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7816 (mmmm) REVERT: D 96 ARG cc_start: 0.8760 (mtt-85) cc_final: 0.8399 (mtt-85) REVERT: E 56 LYS cc_start: 0.9177 (tttm) cc_final: 0.8863 (ttmt) REVERT: E 64 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8590 (mtmt) REVERT: E 120 MET cc_start: 0.8501 (mtp) cc_final: 0.8273 (mtt) REVERT: F 22 LEU cc_start: 0.7870 (mt) cc_final: 0.7428 (mp) REVERT: G 15 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8272 (tttp) REVERT: L 423 ARG cc_start: 0.7827 (tpt170) cc_final: 0.7203 (tpm170) REVERT: L 427 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7083 (mpt) REVERT: M 431 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: M 432 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8504 (mp) outliers start: 12 outliers final: 2 residues processed: 159 average time/residue: 1.7087 time to fit residues: 289.4896 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 : 0.985 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 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 = 0.3549 r_free = 0.3549 target = 0.092966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067950 restraints weight = 25918.336| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.48 r_work: 0.2916 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14074 Z= 0.164 Angle : 0.534 7.039 20215 Z= 0.320 Chirality : 0.033 0.140 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.901 166.461 4236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 2.84 (0.27), residues: 879 helix: 2.66 (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 0.007 0.000 ARG M 396 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 812) hydrogen bonds : angle 2.83075 ( 2065) covalent geometry : bond 0.00357 (14074) covalent geometry : angle 0.53428 (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 163 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8560 (tpt90) cc_final: 0.8336 (tpt-90) REVERT: B 25 ASN cc_start: 0.8777 (m110) cc_final: 0.8571 (m-40) REVERT: D 30 ARG cc_start: 0.7381 (mmt90) cc_final: 0.7124 (mtp180) REVERT: D 31 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7801 (mmmm) REVERT: D 96 ARG cc_start: 0.8761 (mtt-85) cc_final: 0.8404 (mtt-85) REVERT: E 38 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8366 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9129 (tttm) cc_final: 0.8849 (ttmt) REVERT: E 59 GLU cc_start: 0.8567 (pm20) cc_final: 0.8215 (pm20) REVERT: E 64 LYS cc_start: 0.9039 (mmtp) cc_final: 0.8587 (mtmt) REVERT: F 22 LEU cc_start: 0.7844 (mt) cc_final: 0.7413 (mp) REVERT: G 15 LYS cc_start: 0.8790 (ttpp) cc_final: 0.8242 (tttp) REVERT: L 423 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7483 (tpm170) REVERT: M 431 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8397 (mtmm) outliers start: 14 outliers final: 3 residues processed: 154 average time/residue: 1.7772 time to fit residues: 291.4088 Evaluate side-chains 136 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 0.7980 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: 3.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.091234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065872 restraints weight = 25743.926| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.50 r_work: 0.2870 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14074 Z= 0.225 Angle : 0.566 7.154 20215 Z= 0.336 Chirality : 0.035 0.144 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.122 170.717 4236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.84 % Allowed : 11.81 % Favored : 86.35 % 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: 2.80 (0.27), residues: 879 helix: 2.60 (0.20), residues: 625 sheet: None (None), residues: 0 loop : -0.06 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 385 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR D 37 ARG 0.006 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 812) hydrogen bonds : angle 2.90980 ( 2065) covalent geometry : bond 0.00511 (14074) covalent geometry : angle 0.56572 (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 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8895 (tttm) cc_final: 0.8547 (ttpp) REVERT: A 129 ARG cc_start: 0.8572 (tpt90) cc_final: 0.8267 (tpt-90) REVERT: C 73 ASN cc_start: 0.8327 (t160) cc_final: 0.8033 (t160) REVERT: D 31 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7823 (mmmm) REVERT: E 38 PRO cc_start: 0.8571 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9154 (tttm) cc_final: 0.8870 (ttmt) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8262 (pm20) REVERT: E 64 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8608 (mtmt) REVERT: F 22 LEU cc_start: 0.7911 (mt) cc_final: 0.7473 (mp) REVERT: L 432 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (tt) outliers start: 14 outliers final: 5 residues processed: 143 average time/residue: 1.7527 time to fit residues: 266.8161 Evaluate side-chains 138 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 433 ILE 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: 4.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.091980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.066822 restraints weight = 25849.413| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.49 r_work: 0.2893 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1998 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= 0.159 Angle : 0.543 8.095 20215 Z= 0.324 Chirality : 0.033 0.146 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.049 170.547 4236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.49 % Allowed : 12.07 % Favored : 85.43 % 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: 2.90 (0.27), residues: 879 helix: 2.66 (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 0.007 0.001 TRP L 424 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 0.006 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 812) hydrogen bonds : angle 2.86283 ( 2065) covalent geometry : bond 0.00344 (14074) covalent geometry : angle 0.54277 (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 158 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.071 Fit side-chains REVERT: A 56 LYS cc_start: 0.8899 (tttm) cc_final: 0.8541 (ttpp) REVERT: A 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8325 (tpt-90) REVERT: C 73 ASN cc_start: 0.8306 (t0) cc_final: 0.8003 (t160) REVERT: D 31 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7818 (mmmm) REVERT: E 38 PRO cc_start: 0.8584 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9154 (tttm) cc_final: 0.8854 (ttmt) REVERT: E 59 GLU cc_start: 0.8621 (pm20) cc_final: 0.8282 (pm20) REVERT: E 64 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8599 (mtmt) REVERT: F 22 LEU cc_start: 0.7898 (mt) cc_final: 0.7442 (mp) REVERT: G 15 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8098 (tttp) REVERT: L 423 ARG cc_start: 0.7924 (tpt170) cc_final: 0.7689 (tpm170) REVERT: L 432 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7402 (tt) REVERT: M 431 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8399 (mtmm) outliers start: 19 outliers final: 7 residues processed: 147 average time/residue: 1.9677 time to fit residues: 310.1485 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.0050 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.092129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067038 restraints weight = 26020.001| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.47 r_work: 0.2901 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14074 Z= 0.182 Angle : 0.541 8.649 20215 Z= 0.322 Chirality : 0.033 0.141 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.891 171.554 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.57 % Allowed : 12.86 % Favored : 85.56 % 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: 3.01 (0.27), residues: 879 helix: 2.73 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.09 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.007 0.000 ARG L 423 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 812) hydrogen bonds : angle 2.82281 ( 2065) covalent geometry : bond 0.00404 (14074) covalent geometry : angle 0.54099 (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 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.900 Fit side-chains REVERT: A 56 LYS cc_start: 0.8902 (tttm) cc_final: 0.8550 (ttpp) REVERT: A 129 ARG cc_start: 0.8532 (tpt90) cc_final: 0.8317 (tpt-90) REVERT: C 73 ASN cc_start: 0.8378 (t0) cc_final: 0.8037 (t160) REVERT: D 31 LYS cc_start: 0.8382 (mtpp) cc_final: 0.7899 (mmmm) REVERT: E 38 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9137 (tttm) cc_final: 0.8841 (ttmt) REVERT: E 59 GLU cc_start: 0.8609 (pm20) cc_final: 0.8267 (pm20) REVERT: E 64 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8601 (mtmt) REVERT: F 22 LEU cc_start: 0.7913 (mt) cc_final: 0.7487 (mp) REVERT: G 15 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8096 (tttp) REVERT: L 406 ILE cc_start: 0.6450 (mt) cc_final: 0.6085 (tp) REVERT: L 422 ASP cc_start: 0.8199 (m-30) cc_final: 0.7937 (m-30) REVERT: L 423 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7800 (tpp-160) REVERT: M 431 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8409 (mtmm) outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 2.2397 time to fit residues: 343.6012 Evaluate side-chains 139 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067161 restraints weight = 25965.670| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.47 r_work: 0.2903 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2140 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= 0.174 Angle : 0.542 10.047 20215 Z= 0.321 Chirality : 0.033 0.182 2267 Planarity : 0.004 0.045 1542 Dihedral : 29.880 171.846 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.71 % Allowed : 13.91 % Favored : 84.38 % 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: 2.76 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.10 (0.34), residues: 254 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 0.011 0.001 TYR D 37 ARG 0.009 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 812) hydrogen bonds : angle 2.82934 ( 2065) covalent geometry : bond 0.00384 (14074) covalent geometry : angle 0.54197 (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 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.052 Fit side-chains REVERT: A 56 LYS cc_start: 0.8903 (tttm) cc_final: 0.8548 (ttpp) REVERT: A 129 ARG cc_start: 0.8531 (tpt90) cc_final: 0.8295 (tpt-90) REVERT: C 73 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8016 (t160) REVERT: D 31 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7882 (mmmm) REVERT: E 38 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9126 (tttm) cc_final: 0.8835 (ttmt) REVERT: E 59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8275 (pm20) REVERT: E 64 LYS cc_start: 0.9054 (mmtp) cc_final: 0.8601 (mtmt) REVERT: F 22 LEU cc_start: 0.7863 (mt) cc_final: 0.7448 (mp) REVERT: L 422 ASP cc_start: 0.8197 (m-30) cc_final: 0.7902 (m-30) REVERT: L 423 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7773 (tpp-160) REVERT: L 432 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7435 (tt) REVERT: M 431 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8401 (mtmm) outliers start: 13 outliers final: 6 residues processed: 145 average time/residue: 1.7513 time to fit residues: 270.3426 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 23 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.092683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067564 restraints weight = 26107.645| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.48 r_work: 0.2912 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14074 Z= 0.151 Angle : 0.537 10.549 20215 Z= 0.319 Chirality : 0.032 0.142 2267 Planarity : 0.004 0.040 1542 Dihedral : 29.875 171.885 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.97 % Allowed : 14.04 % 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: 3.12 (0.27), residues: 879 helix: 2.84 (0.20), residues: 623 sheet: None (None), residues: 0 loop : 0.10 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 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 0.006 0.000 ARG L 423 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 812) hydrogen bonds : angle 2.82175 ( 2065) covalent geometry : bond 0.00324 (14074) covalent geometry : angle 0.53689 (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 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.130 Fit side-chains REVERT: A 56 LYS cc_start: 0.8894 (tttm) cc_final: 0.8543 (ttpp) REVERT: A 129 ARG cc_start: 0.8516 (tpt90) cc_final: 0.8287 (tpt-90) REVERT: C 73 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8004 (t160) REVERT: D 31 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7870 (mmmm) REVERT: E 38 PRO cc_start: 0.8487 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9126 (tttm) cc_final: 0.8866 (ttmp) REVERT: E 59 GLU cc_start: 0.8610 (pm20) cc_final: 0.8267 (pm20) REVERT: E 64 LYS cc_start: 0.9050 (mmtp) cc_final: 0.8596 (mtmt) REVERT: F 22 LEU cc_start: 0.7865 (mt) cc_final: 0.7432 (mp) REVERT: G 15 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8036 (tttp) REVERT: L 422 ASP cc_start: 0.8213 (m-30) cc_final: 0.7938 (m-30) REVERT: L 423 ARG cc_start: 0.8030 (tpt170) cc_final: 0.7752 (tpp-160) REVERT: L 432 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7425 (tt) REVERT: M 431 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8395 (mtmm) outliers start: 15 outliers final: 6 residues processed: 141 average time/residue: 1.7339 time to fit residues: 260.8331 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 68 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.092678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067550 restraints weight = 25823.550| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.50 r_work: 0.2911 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14074 Z= 0.160 Angle : 0.537 10.860 20215 Z= 0.318 Chirality : 0.032 0.154 2267 Planarity : 0.004 0.039 1542 Dihedral : 29.851 172.018 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.71 % Allowed : 14.30 % 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: 3.10 (0.27), residues: 879 helix: 2.82 (0.20), residues: 623 sheet: None (None), residues: 0 loop : 0.10 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 383 HIS 0.003 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 0.03761 ( 812) hydrogen bonds : angle 2.81319 ( 2065) covalent geometry : bond 0.00349 (14074) covalent geometry : angle 0.53722 (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 149 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.861 Fit side-chains REVERT: A 56 LYS cc_start: 0.8892 (tttm) cc_final: 0.8547 (ttpp) REVERT: A 129 ARG cc_start: 0.8504 (tpt90) cc_final: 0.8274 (tpt-90) REVERT: C 73 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7998 (t160) REVERT: D 31 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7799 (mmmm) REVERT: E 38 PRO cc_start: 0.8487 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9130 (tttm) cc_final: 0.8872 (ttmp) REVERT: E 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8255 (pm20) REVERT: E 64 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8593 (mtmt) REVERT: F 22 LEU cc_start: 0.7861 (mt) cc_final: 0.7433 (mp) REVERT: G 15 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8017 (tttp) REVERT: L 422 ASP cc_start: 0.8212 (m-30) cc_final: 0.7933 (m-30) REVERT: L 423 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7743 (tpp-160) REVERT: M 431 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8406 (mtmm) outliers start: 13 outliers final: 5 residues processed: 141 average time/residue: 2.2298 time to fit residues: 334.8913 Evaluate side-chains 142 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.091140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.065885 restraints weight = 25605.711| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.46 r_work: 0.2869 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14074 Z= 0.237 Angle : 0.575 10.617 20215 Z= 0.337 Chirality : 0.036 0.147 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.024 175.029 4236 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.18 % Allowed : 14.83 % 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: 2.90 (0.27), residues: 879 helix: 2.65 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.06 (0.34), 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 0.010 0.001 TYR D 37 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 812) hydrogen bonds : angle 2.92387 ( 2065) covalent geometry : bond 0.00540 (14074) covalent geometry : angle 0.57548 (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 149 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.011 Fit side-chains REVERT: A 56 LYS cc_start: 0.8920 (tttm) cc_final: 0.8573 (ttpp) REVERT: A 64 LYS cc_start: 0.8887 (mttp) cc_final: 0.8424 (mtpt) REVERT: A 129 ARG cc_start: 0.8530 (tpt90) cc_final: 0.8276 (tpt-90) REVERT: C 73 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8092 (t160) REVERT: D 31 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7773 (mmmm) REVERT: E 38 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8256 (Cg_endo) REVERT: E 56 LYS cc_start: 0.9147 (tttm) cc_final: 0.8839 (ttmt) REVERT: E 59 GLU cc_start: 0.8629 (pm20) cc_final: 0.8269 (pm20) REVERT: E 64 LYS cc_start: 0.9073 (mmtp) cc_final: 0.8606 (mtmt) REVERT: F 22 LEU cc_start: 0.7871 (mt) cc_final: 0.7446 (mp) REVERT: L 406 ILE cc_start: 0.6396 (mt) cc_final: 0.5987 (tp) REVERT: L 422 ASP cc_start: 0.8203 (m-30) cc_final: 0.7920 (m-30) REVERT: M 431 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8375 (mtmm) outliers start: 9 outliers final: 5 residues processed: 143 average time/residue: 1.8673 time to fit residues: 283.7701 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS 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: 0.8980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.091722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066445 restraints weight = 25868.104| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.49 r_work: 0.2888 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2174 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= 0.169 Angle : 0.563 11.029 20215 Z= 0.331 Chirality : 0.033 0.147 2267 Planarity : 0.004 0.060 1542 Dihedral : 30.036 175.144 4236 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.31 % Allowed : 15.35 % 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: 2.99 (0.27), residues: 879 helix: 2.71 (0.20), residues: 625 sheet: None (None), residues: 0 loop : 0.09 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 383 HIS 0.005 0.001 HIS F 75 PHE 0.005 0.001 PHE E 78 TYR 0.011 0.001 TYR D 37 ARG 0.009 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 812) hydrogen bonds : angle 2.92967 ( 2065) covalent geometry : bond 0.00371 (14074) covalent geometry : angle 0.56311 (20215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12256.36 seconds wall clock time: 215 minutes 6.04 seconds (12906.04 seconds total)