Starting phenix.real_space_refine on Tue Aug 4 18:24:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.map" model { file = "/net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgw_55912/08_2026/9tgw_55912.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 24 5.49 5 S 33 5.16 5 C 3585 2.51 5 N 981 2.21 5 O 1207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5830 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 273 Chain: "P" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" 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: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.04, per 1000 atoms: 0.18 Number of scatterers: 5830 At special positions: 0 Unit cell: (92.72, 98.04, 111.72, 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 33 16.00 P 24 15.00 O 1207 8.00 N 981 7.00 C 3585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 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: 0.42 Conformation dependent library (CDL) restraints added in 186.0 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 7.3% alpha, 44.8% beta 12 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.706A pdb=" N THR A 31 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.721A pdb=" N ASP A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.029A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.726A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.890A pdb=" N THR C 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.562A pdb=" N THR D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.809A pdb=" N THR D 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.771A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.842A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.654A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.118A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.737A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.962A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.307A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.307A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 111 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.554A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.553A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.339A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.339A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1790 1.35 - 1.46: 1689 1.46 - 1.58: 2408 1.58 - 1.70: 47 1.70 - 1.82: 54 Bond restraints: 5988 Sorted by residual: bond pdb=" C3' DG O 6 " pdb=" C2' DG O 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG P 6 " pdb=" C2' DG P 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+00 bond pdb=" C3' DG P 2 " pdb=" C2' DG P 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C3' DG O 10 " pdb=" C2' DG O 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DG O 2 " pdb=" C2' DG O 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.27e+00 ... (remaining 5983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 7964 1.31 - 2.63: 194 2.63 - 3.94: 26 3.94 - 5.26: 13 5.26 - 6.57: 3 Bond angle restraints: 8200 Sorted by residual: angle pdb=" O4' DG O 8 " pdb=" C4' DG O 8 " pdb=" C3' DG O 8 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.36e+01 angle pdb=" O4' DG P 4 " pdb=" C1' DG P 4 " pdb=" C2' DG P 4 " ideal model delta sigma weight residual 105.90 108.83 -2.93 8.00e-01 1.56e+00 1.35e+01 angle pdb=" O4' DC O 9 " pdb=" C4' DC O 9 " pdb=" C3' DC O 9 " ideal model delta sigma weight residual 106.00 103.84 2.16 6.00e-01 2.78e+00 1.30e+01 angle pdb=" C3' DG O 8 " pdb=" O3' DG O 8 " pdb=" P DC O 9 " ideal model delta sigma weight residual 119.70 123.80 -4.10 1.20e+00 6.94e-01 1.17e+01 angle pdb=" C3' DG P 8 " pdb=" O3' DG P 8 " pdb=" P DC P 9 " ideal model delta sigma weight residual 119.70 123.56 -3.86 1.20e+00 6.94e-01 1.03e+01 ... (remaining 8195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.99: 3142 29.99 - 59.99: 290 59.99 - 89.98: 26 89.98 - 119.98: 1 119.98 - 149.97: 1 Dihedral angle restraints: 3460 sinusoidal: 1486 harmonic: 1974 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 137.63 -44.63 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA LYS F 93 " pdb=" C LYS F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta harmonic sigma weight residual 180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LYS E 93 " pdb=" C LYS E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual 180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 570 0.033 - 0.066: 193 0.066 - 0.099: 78 0.099 - 0.132: 40 0.132 - 0.165: 5 Chirality restraints: 886 Sorted by residual: chirality pdb=" CA PHE E 94 " pdb=" N PHE E 94 " pdb=" C PHE E 94 " pdb=" CB PHE E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA PHE F 94 " pdb=" N PHE F 94 " pdb=" C PHE F 94 " pdb=" CB PHE F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE B 94 " pdb=" N PHE B 94 " pdb=" C PHE B 94 " pdb=" CB PHE B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 883 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 79 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 80 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 94 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO E 95 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 39 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO F 40 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO F 40 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 40 " -0.017 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1460 2.80 - 3.32: 4319 3.32 - 3.85: 9193 3.85 - 4.37: 11260 4.37 - 4.90: 19763 Nonbonded interactions: 45995 Sorted by model distance: nonbonded pdb=" O SER D 121 " pdb=" OG SER D 121 " model vdw 2.270 3.040 nonbonded pdb=" NH2 ARG F 61 " pdb=" OD1 ASP F 82 " model vdw 2.344 3.120 nonbonded pdb=" NH2 ARG B 61 " pdb=" OD2 ASP B 82 " model vdw 2.377 3.120 nonbonded pdb=" O ILE B 29 " pdb=" OH TYR B 71 " model vdw 2.418 3.040 nonbonded pdb=" O TYR F 50 " pdb=" OG1 THR F 51 " model vdw 2.446 3.040 ... (remaining 45990 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'O' and (resid 1 through 5 or resid 7 through 12)) selection = (chain 'P' and (resid 1 through 5 or resid 7 through 12)) } 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=0.02 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.003 0.027 5994 Z= 0.255 Angle : 0.531 6.570 8212 Z= 0.356 Chirality : 0.044 0.165 886 Planarity : 0.004 0.040 960 Dihedral : 20.067 149.970 2194 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.61 % Allowed : 29.73 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.33), residues: 669 helix: None (None), residues: 0 sheet: 0.52 (0.30), residues: 327 loop : -0.48 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.011 0.001 TYR F 91 PHE 0.020 0.001 PHE F 94 TRP 0.004 0.001 TRP D 112 HIS 0.000 0.000 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.26 ( 5988) covalent geometry : angle 0.53084 / 0.36 ( 8200) SS BOND : bond 0.00419 / 0.20 ( 6) SS BOND : angle 0.70638 / 0.37 ( 12) hydrogen bonds : bond 0.21962 / 14.65 ( 224) hydrogen bonds : angle 8.11182 / 5.66 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: E 3 GLN cc_start: 0.7222 (mp10) cc_final: 0.6944 (mp-120) REVERT: E 97 THR cc_start: 0.6741 (p) cc_final: 0.6530 (p) REVERT: F 43 THR cc_start: 0.7675 (m) cc_final: 0.7443 (p) outliers start: 21 outliers final: 4 residues processed: 168 average time/residue: 0.3706 time to fit residues: 65.5261 Evaluate side-chains 107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 67 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 84 GLN A 101 GLN C 35 ASN D 79 ASN E 27 GLN E 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114161 restraints weight = 6674.317| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.88 r_work: 0.3291 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5994 Z= 0.197 Angle : 0.705 6.875 8212 Z= 0.393 Chirality : 0.051 0.343 886 Planarity : 0.005 0.042 960 Dihedral : 16.109 153.828 995 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 6.70 % Allowed : 28.35 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.57 (0.29), residues: 336 loop : -0.71 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 61 TYR 0.019 0.002 TYR A 62 PHE 0.034 0.003 PHE B 94 TRP 0.014 0.002 TRP A 47 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 ( 5988) covalent geometry : angle 0.70364 / 0.39 ( 8200) SS BOND : bond 0.00660 / 0.31 ( 6) SS BOND : angle 1.22195 / 0.62 ( 12) hydrogen bonds : bond 0.03924 / 2.64 ( 224) hydrogen bonds : angle 5.45448 / 3.79 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.332 Fit side-chains REVERT: B 15 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5955 (tp) REVERT: C 43 LYS cc_start: 0.7643 (mppt) cc_final: 0.7321 (mmtm) REVERT: C 60 THR cc_start: 0.8292 (p) cc_final: 0.8026 (p) REVERT: C 110 ASP cc_start: 0.7405 (p0) cc_final: 0.6822 (p0) REVERT: D 100 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8052 (ttm170) REVERT: E 3 GLN cc_start: 0.7692 (mp10) cc_final: 0.7316 (mp-120) REVERT: E 104 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6849 (mp) REVERT: F 60 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7522 (p) REVERT: F 72 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8258 (p) outliers start: 39 outliers final: 8 residues processed: 154 average time/residue: 0.3413 time to fit residues: 55.5403 Evaluate side-chains 125 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 101 GLN B 31 ASN C 39 GLN D 57 ASN E 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108442 restraints weight = 6189.300| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.50 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5994 Z= 0.133 Angle : 0.578 7.221 8212 Z= 0.327 Chirality : 0.047 0.378 886 Planarity : 0.004 0.048 960 Dihedral : 15.967 147.830 991 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.47 % Allowed : 30.07 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.58 (0.29), residues: 342 loop : -0.44 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.014 0.001 TYR D 97 PHE 0.021 0.002 PHE B 94 TRP 0.006 0.001 TRP C 112 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 5988) covalent geometry : angle 0.57775 / 0.33 ( 8200) SS BOND : bond 0.00480 / 0.21 ( 6) SS BOND : angle 0.73695 / 0.45 ( 12) hydrogen bonds : bond 0.04039 / 2.66 ( 224) hydrogen bonds : angle 4.91420 / 3.40 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.156 Fit side-chains REVERT: A 11 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 46 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7828 (tt0) REVERT: B 15 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6175 (tp) REVERT: C 43 LYS cc_start: 0.7797 (mppt) cc_final: 0.7487 (mmtm) REVERT: C 73 SER cc_start: 0.8273 (p) cc_final: 0.8057 (p) REVERT: C 80 MET cc_start: 0.8571 (mmp) cc_final: 0.8352 (tpp) REVERT: D 100 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8131 (ttm170) REVERT: E 3 GLN cc_start: 0.8068 (mp10) cc_final: 0.7787 (mp-120) REVERT: F 56 SER cc_start: 0.8143 (m) cc_final: 0.7795 (t) REVERT: F 60 SER cc_start: 0.8042 (t) cc_final: 0.7792 (p) REVERT: F 81 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6970 (pm20) outliers start: 26 outliers final: 8 residues processed: 137 average time/residue: 0.3967 time to fit residues: 56.9665 Evaluate side-chains 122 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN D 30 ASN D 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099998 restraints weight = 6231.296| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.91 r_work: 0.2986 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5994 Z= 0.264 Angle : 0.851 11.150 8212 Z= 0.469 Chirality : 0.058 0.513 886 Planarity : 0.005 0.042 960 Dihedral : 16.142 155.571 991 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.74 % Favored : 96.11 % Rotamer: Outliers : 7.04 % Allowed : 28.18 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.28 (0.28), residues: 360 loop : -0.66 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 61 TYR 0.020 0.003 TYR C 97 PHE 0.036 0.004 PHE F 94 TRP 0.012 0.002 TRP A 47 HIS 0.006 0.003 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 ( 5988) covalent geometry : angle 0.84652 / 0.47 ( 8200) SS BOND : bond 0.01316 / 0.60 ( 6) SS BOND : angle 2.35575 / 1.35 ( 12) hydrogen bonds : bond 0.05404 / 3.58 ( 224) hydrogen bonds : angle 5.20515 / 3.64 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.124 Fit side-chains REVERT: A 46 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8008 (tt0) REVERT: B 15 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6608 (tp) REVERT: B 24 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8571 (p) REVERT: C 43 LYS cc_start: 0.8093 (mppt) cc_final: 0.7744 (mmtm) REVERT: D 3 GLN cc_start: 0.8568 (mt0) cc_final: 0.8259 (mt0) REVERT: D 72 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8325 (tt) REVERT: D 111 TYR cc_start: 0.8254 (m-80) cc_final: 0.8025 (m-80) REVERT: E 104 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7916 (mp) REVERT: F 47 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8627 (mp) REVERT: F 81 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7548 (pm20) outliers start: 41 outliers final: 14 residues processed: 148 average time/residue: 0.3401 time to fit residues: 53.0065 Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 0.0010 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN D 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.099679 restraints weight = 6417.418| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.91 r_work: 0.2996 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5994 Z= 0.194 Angle : 0.658 7.771 8212 Z= 0.373 Chirality : 0.052 0.439 886 Planarity : 0.004 0.037 960 Dihedral : 16.144 152.609 991 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.73 % Allowed : 27.32 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.36 (0.28), residues: 360 loop : -0.58 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.016 0.002 TYR D 97 PHE 0.037 0.003 PHE F 94 TRP 0.006 0.001 TRP A 36 HIS 0.004 0.002 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 5988) covalent geometry : angle 0.65590 / 0.37 ( 8200) SS BOND : bond 0.00729 / 0.32 ( 6) SS BOND : angle 1.61729 / 0.88 ( 12) hydrogen bonds : bond 0.04072 / 2.70 ( 224) hydrogen bonds : angle 4.93508 / 3.43 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.128 Fit side-chains REVERT: A 15 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8482 (mttt) REVERT: A 46 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7978 (tt0) REVERT: C 43 LYS cc_start: 0.8103 (mppt) cc_final: 0.7733 (mmtm) REVERT: D 3 GLN cc_start: 0.8502 (mt0) cc_final: 0.8233 (mt0) REVERT: D 72 ILE cc_start: 0.8671 (pt) cc_final: 0.8418 (tt) REVERT: E 73 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8330 (tp) REVERT: F 81 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7500 (pm20) outliers start: 45 outliers final: 20 residues processed: 143 average time/residue: 0.3633 time to fit residues: 54.9225 Evaluate side-chains 131 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN D 114 GLN F 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100650 restraints weight = 6293.939| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.89 r_work: 0.3011 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5994 Z= 0.149 Angle : 0.610 7.397 8212 Z= 0.347 Chirality : 0.049 0.383 886 Planarity : 0.004 0.040 960 Dihedral : 16.079 151.456 991 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.01 % Allowed : 28.01 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.44 (0.28), residues: 360 loop : -0.45 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.014 0.002 TYR D 97 PHE 0.031 0.003 PHE F 94 TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 5988) covalent geometry : angle 0.60649 / 0.35 ( 8200) SS BOND : bond 0.00742 / 0.35 ( 6) SS BOND : angle 1.80211 / 0.95 ( 12) hydrogen bonds : bond 0.03459 / 2.30 ( 224) hydrogen bonds : angle 4.73297 / 3.28 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.181 Fit side-chains REVERT: A 15 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8439 (mttt) REVERT: A 46 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: B 54 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9054 (mp) REVERT: C 43 LYS cc_start: 0.8086 (mppt) cc_final: 0.7733 (mmtm) REVERT: D 3 GLN cc_start: 0.8499 (mt0) cc_final: 0.8214 (mt0) REVERT: E 73 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8343 (tp) REVERT: F 3 GLN cc_start: 0.8211 (mp10) cc_final: 0.7548 (mm-40) REVERT: F 47 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8560 (mp) REVERT: F 81 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7497 (pm20) outliers start: 35 outliers final: 20 residues processed: 133 average time/residue: 0.3710 time to fit residues: 52.2495 Evaluate side-chains 132 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101840 restraints weight = 6286.791| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.91 r_work: 0.3032 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5994 Z= 0.119 Angle : 0.558 6.916 8212 Z= 0.319 Chirality : 0.047 0.350 886 Planarity : 0.004 0.039 960 Dihedral : 16.036 150.445 991 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.98 % Allowed : 29.55 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.48 (0.28), residues: 360 loop : -0.38 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.012 0.001 TYR D 97 PHE 0.027 0.002 PHE F 94 TRP 0.006 0.001 TRP D 47 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 5988) covalent geometry : angle 0.55633 / 0.32 ( 8200) SS BOND : bond 0.00561 / 0.26 ( 6) SS BOND : angle 1.29617 / 0.68 ( 12) hydrogen bonds : bond 0.03000 / 2.00 ( 224) hydrogen bonds : angle 4.59966 / 3.16 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.196 Fit side-chains REVERT: A 15 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8446 (mttt) REVERT: A 46 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7968 (tt0) REVERT: A 87 ASN cc_start: 0.8877 (t0) cc_final: 0.8620 (t0) REVERT: B 61 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7678 (mtm110) REVERT: C 43 LYS cc_start: 0.8057 (mppt) cc_final: 0.7720 (mmtm) REVERT: D 3 GLN cc_start: 0.8506 (mt0) cc_final: 0.8204 (mt0) REVERT: E 73 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8312 (tp) REVERT: F 3 GLN cc_start: 0.8283 (mp10) cc_final: 0.7610 (mm-40) outliers start: 29 outliers final: 13 residues processed: 129 average time/residue: 0.4228 time to fit residues: 57.5266 Evaluate side-chains 118 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 103 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102160 restraints weight = 6263.566| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.90 r_work: 0.3033 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5994 Z= 0.117 Angle : 0.551 7.176 8212 Z= 0.315 Chirality : 0.047 0.355 886 Planarity : 0.004 0.041 960 Dihedral : 15.969 149.462 991 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.64 % Allowed : 29.73 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.51 (0.27), residues: 360 loop : -0.32 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.012 0.001 TYR D 97 PHE 0.026 0.002 PHE F 94 TRP 0.006 0.001 TRP D 47 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 ( 5988) covalent geometry : angle 0.55001 / 0.32 ( 8200) SS BOND : bond 0.00579 / 0.26 ( 6) SS BOND : angle 1.12502 / 0.61 ( 12) hydrogen bonds : bond 0.02919 / 1.95 ( 224) hydrogen bonds : angle 4.50841 / 3.08 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.216 Fit side-chains REVERT: A 13 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7048 (mp10) REVERT: A 15 LYS cc_start: 0.8773 (mtmt) cc_final: 0.8454 (mttt) REVERT: A 46 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 87 ASN cc_start: 0.8832 (t0) cc_final: 0.8577 (t0) REVERT: B 61 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7620 (mtm110) REVERT: C 43 LYS cc_start: 0.8043 (mppt) cc_final: 0.7701 (mmtm) REVERT: D 3 GLN cc_start: 0.8513 (mt0) cc_final: 0.8203 (mt0) REVERT: E 73 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8335 (tp) REVERT: E 103 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8008 (tptp) REVERT: F 3 GLN cc_start: 0.8310 (mp10) cc_final: 0.7643 (mm-40) REVERT: F 38 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.9142 (tt0) REVERT: F 47 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8511 (mp) REVERT: F 81 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7433 (pm20) outliers start: 27 outliers final: 17 residues processed: 129 average time/residue: 0.4252 time to fit residues: 57.6713 Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 103 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099981 restraints weight = 6292.560| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.89 r_work: 0.2996 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5994 Z= 0.161 Angle : 0.625 7.991 8212 Z= 0.353 Chirality : 0.050 0.409 886 Planarity : 0.004 0.040 960 Dihedral : 15.947 148.895 991 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.98 % Allowed : 30.07 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.47 (0.27), residues: 360 loop : -0.32 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.016 0.002 TYR D 97 PHE 0.035 0.003 PHE F 94 TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 5988) covalent geometry : angle 0.62218 / 0.35 ( 8200) SS BOND : bond 0.00853 / 0.40 ( 6) SS BOND : angle 1.66902 / 0.92 ( 12) hydrogen bonds : bond 0.03622 / 2.40 ( 224) hydrogen bonds : angle 4.58639 / 3.15 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.217 Fit side-chains REVERT: A 13 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7050 (mp10) REVERT: A 15 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8527 (mtmm) REVERT: A 46 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: A 87 ASN cc_start: 0.8892 (t0) cc_final: 0.8643 (t0) REVERT: B 61 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7632 (mtm110) REVERT: C 43 LYS cc_start: 0.8127 (mppt) cc_final: 0.7773 (mmtm) REVERT: D 3 GLN cc_start: 0.8513 (mt0) cc_final: 0.8209 (mt0) REVERT: E 73 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8423 (tp) REVERT: E 103 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8014 (tptp) REVERT: F 3 GLN cc_start: 0.8352 (mp10) cc_final: 0.7708 (mm-40) REVERT: F 47 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8547 (mp) REVERT: F 81 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7523 (pm20) outliers start: 29 outliers final: 18 residues processed: 126 average time/residue: 0.4425 time to fit residues: 58.7362 Evaluate side-chains 127 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN F 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101492 restraints weight = 6278.934| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.77 r_work: 0.3045 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5994 Z= 0.120 Angle : 0.557 6.953 8212 Z= 0.319 Chirality : 0.047 0.343 886 Planarity : 0.004 0.039 960 Dihedral : 16.000 149.601 991 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.78 % Allowed : 31.27 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.51 (0.28), residues: 360 loop : -0.28 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 50 TYR 0.012 0.001 TYR D 97 PHE 0.025 0.002 PHE F 94 TRP 0.008 0.001 TRP D 47 HIS 0.001 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 5988) covalent geometry : angle 0.55642 / 0.32 ( 8200) SS BOND : bond 0.00561 / 0.27 ( 6) SS BOND : angle 1.06074 / 0.60 ( 12) hydrogen bonds : bond 0.02989 / 1.99 ( 224) hydrogen bonds : angle 4.54402 / 3.11 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.221 Fit side-chains REVERT: A 13 GLN cc_start: 0.7314 (mm-40) cc_final: 0.7026 (mp10) REVERT: A 15 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8519 (mtmm) REVERT: A 46 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: A 87 ASN cc_start: 0.8820 (t0) cc_final: 0.8580 (t0) REVERT: B 61 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7629 (mtm110) REVERT: C 43 LYS cc_start: 0.8085 (mppt) cc_final: 0.7768 (mmtm) REVERT: D 3 GLN cc_start: 0.8495 (mt0) cc_final: 0.8192 (mt0) REVERT: E 73 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8365 (tp) REVERT: E 103 LYS cc_start: 0.8625 (ttpp) cc_final: 0.7943 (tptp) REVERT: F 3 GLN cc_start: 0.8346 (mp10) cc_final: 0.7750 (mm-40) REVERT: F 47 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8522 (mp) REVERT: F 81 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7445 (pm20) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 0.4288 time to fit residues: 54.6940 Evaluate side-chains 123 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100871 restraints weight = 6233.196| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.88 r_work: 0.3012 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5994 Z= 0.136 Angle : 0.589 7.566 8212 Z= 0.335 Chirality : 0.048 0.379 886 Planarity : 0.004 0.041 960 Dihedral : 15.941 148.703 991 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.12 % Allowed : 31.10 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.32), residues: 669 helix: None (None), residues: 0 sheet: 0.51 (0.28), residues: 360 loop : -0.26 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.015 0.001 TYR D 97 PHE 0.032 0.002 PHE F 94 TRP 0.008 0.001 TRP D 47 HIS 0.002 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 5988) covalent geometry : angle 0.58703 / 0.33 ( 8200) SS BOND : bond 0.00720 / 0.34 ( 6) SS BOND : angle 1.41031 / 0.78 ( 12) hydrogen bonds : bond 0.03242 / 2.15 ( 224) hydrogen bonds : angle 4.50129 / 3.09 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.07 seconds wall clock time: 40 minutes 38.18 seconds (2438.18 seconds total)