Starting phenix.real_space_refine on Fri Aug 22 12:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az4_15753/08_2025/8az4_15753.map" } resolution = 2.2 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 420 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2280 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 1.44, per 1000 atoms: 0.63 Number of scatterers: 2280 At special positions: 0 Unit cell: (69.3, 72.9, 45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 510 8.00 N 420 7.00 C 1350 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 163.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.979A pdb=" N ASN A 21 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN C 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASN C 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN E 22 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN G 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN G 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN I 22 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22 removed outlier: 6.937A pdb=" N ASN B 21 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN D 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN D 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN F 21 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN H 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN H 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN J 22 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.599A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.36 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 340 1.28 - 1.35: 400 1.35 - 1.41: 290 1.41 - 1.48: 320 1.48 - 1.54: 870 Bond restraints: 2220 Sorted by residual: bond pdb=" CG ASN E 35 " pdb=" ND2 ASN E 35 " ideal model delta sigma weight residual 1.328 1.312 0.016 2.10e-02 2.27e+03 6.10e-01 bond pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 6.06e-01 bond pdb=" CD2 TYR C 37 " pdb=" CE2 TYR C 37 " ideal model delta sigma weight residual 1.382 1.359 0.023 3.00e-02 1.11e+03 5.75e-01 bond pdb=" CG1 ILE I 26 " pdb=" CD1 ILE I 26 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.65e-01 bond pdb=" CG ASN F 31 " pdb=" OD1 ASN F 31 " ideal model delta sigma weight residual 1.231 1.217 0.014 1.90e-02 2.77e+03 5.56e-01 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 2571 0.95 - 1.90: 373 1.90 - 2.85: 59 2.85 - 3.80: 12 3.80 - 4.75: 5 Bond angle restraints: 3020 Sorted by residual: angle pdb=" N THR C 30 " pdb=" CA THR C 30 " pdb=" C THR C 30 " ideal model delta sigma weight residual 109.40 112.94 -3.54 1.63e+00 3.76e-01 4.71e+00 angle pdb=" N THR I 30 " pdb=" CA THR I 30 " pdb=" C THR I 30 " ideal model delta sigma weight residual 109.24 112.77 -3.53 1.67e+00 3.59e-01 4.46e+00 angle pdb=" N THR G 30 " pdb=" CA THR G 30 " pdb=" C THR G 30 " ideal model delta sigma weight residual 109.40 112.77 -3.37 1.63e+00 3.76e-01 4.27e+00 angle pdb=" N THR A 30 " pdb=" CA THR A 30 " pdb=" C THR A 30 " ideal model delta sigma weight residual 109.40 112.76 -3.36 1.63e+00 3.76e-01 4.26e+00 angle pdb=" N SER F 34 " pdb=" CA SER F 34 " pdb=" C SER F 34 " ideal model delta sigma weight residual 111.54 114.31 -2.77 1.36e+00 5.41e-01 4.14e+00 ... (remaining 3015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.77: 1130 10.77 - 21.54: 86 21.54 - 32.31: 29 32.31 - 43.08: 10 43.08 - 53.85: 5 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" CA LEU I 27 " pdb=" CB LEU I 27 " pdb=" CG LEU I 27 " pdb=" CD1 LEU I 27 " ideal model delta sinusoidal sigma weight residual 180.00 146.98 33.02 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU E 27 " pdb=" CB LEU E 27 " pdb=" CG LEU E 27 " pdb=" CD1 LEU E 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.02 32.98 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU G 27 " pdb=" CB LEU G 27 " pdb=" CG LEU G 27 " pdb=" CD1 LEU G 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.07 32.93 3 1.50e+01 4.44e-03 5.46e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 162 0.031 - 0.062: 114 0.062 - 0.093: 21 0.093 - 0.124: 31 0.124 - 0.155: 12 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 337 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 27 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LEU G 27 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU G 27 " -0.008 2.00e-02 2.50e+03 pdb=" N SER G 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 29 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C SER C 29 " 0.019 2.00e-02 2.50e+03 pdb=" O SER C 29 " -0.007 2.00e-02 2.50e+03 pdb=" N THR C 30 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 27 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C LEU E 27 " 0.018 2.00e-02 2.50e+03 pdb=" O LEU E 27 " -0.007 2.00e-02 2.50e+03 pdb=" N SER E 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 525 2.81 - 3.34: 1772 3.34 - 3.86: 4197 3.86 - 4.38: 4580 4.38 - 4.90: 8397 Nonbonded interactions: 19471 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" O HOH D 101 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O HOH C 101 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" O HOH E 101 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR J 37 " pdb=" O HOH J 101 " model vdw 2.322 3.040 nonbonded pdb=" OG SER J 19 " pdb=" O HOH J 102 " model vdw 2.335 3.040 ... (remaining 19466 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=0.97 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: 1.730 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 0.106 2230 Z= 0.764 Angle : 0.720 4.752 3020 Z= 0.431 Chirality : 0.053 0.155 340 Planarity : 0.003 0.012 400 Dihedral : 10.223 53.851 740 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.94 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 11 TYR 0.010 0.002 TYR E 37 PHE 0.013 0.002 PHE E 15 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 2220) covalent geometry : angle 0.72032 ( 3020) hydrogen bonds : bond 0.15728 ( 101) hydrogen bonds : angle 7.13756 ( 295) Misc. bond : bond 0.10548 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.094 Fit side-chains REVERT: B 11 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7266 (mmt180) REVERT: I 11 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7553 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.7071 time to fit residues: 23.7766 Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 18 HIS A H 21 ASN I 18 HIS A I 21 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.098634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071718 restraints weight = 12392.287| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.83 r_work: 0.3066 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2230 Z= 0.136 Angle : 0.622 5.923 3020 Z= 0.326 Chirality : 0.047 0.135 340 Planarity : 0.002 0.012 400 Dihedral : 4.232 10.401 310 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.42 % Allowed : 10.83 % Favored : 88.75 % 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 aren not related in a simple way. whole: -3.75 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 11 TYR 0.003 0.001 TYR I 37 PHE 0.010 0.002 PHE H 15 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2220) covalent geometry : angle 0.62233 ( 3020) hydrogen bonds : bond 0.04970 ( 101) hydrogen bonds : angle 5.40654 ( 295) Misc. bond : bond 0.00084 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7648 (mtm-85) REVERT: I 11 ARG cc_start: 0.8536 (mtt180) cc_final: 0.8036 (mtm-85) REVERT: J 11 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.7684 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.5767 time to fit residues: 19.4871 Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070183 restraints weight = 15184.154| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.97 r_work: 0.3030 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2230 Z= 0.209 Angle : 0.715 6.322 3020 Z= 0.375 Chirality : 0.049 0.138 340 Planarity : 0.003 0.008 400 Dihedral : 4.237 10.672 310 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.50 % Allowed : 9.58 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.005 0.001 TYR C 37 PHE 0.012 0.002 PHE H 15 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2220) covalent geometry : angle 0.71513 ( 3020) hydrogen bonds : bond 0.05838 ( 101) hydrogen bonds : angle 5.62008 ( 295) Misc. bond : bond 0.00130 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (mmm-85) REVERT: D 11 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7805 (mmm-85) REVERT: G 11 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7778 (mtm-85) REVERT: H 16 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8567 (tt) REVERT: I 11 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8077 (mtm-85) REVERT: J 11 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7680 (mtm-85) outliers start: 6 outliers final: 0 residues processed: 29 average time/residue: 0.7515 time to fit residues: 22.2040 Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070106 restraints weight = 17575.739| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.09 r_work: 0.3024 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2230 Z= 0.192 Angle : 0.680 6.603 3020 Z= 0.356 Chirality : 0.048 0.136 340 Planarity : 0.002 0.008 400 Dihedral : 4.219 10.315 310 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.08 % Allowed : 9.58 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.005 0.001 TYR C 37 PHE 0.011 0.002 PHE H 15 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2220) covalent geometry : angle 0.67965 ( 3020) hydrogen bonds : bond 0.05405 ( 101) hydrogen bonds : angle 5.49902 ( 295) Misc. bond : bond 0.00126 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8207 (mmm-85) REVERT: G 11 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7787 (mtm-85) REVERT: H 16 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8580 (tt) REVERT: I 11 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8077 (mtm-85) REVERT: J 11 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7706 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 0.7083 time to fit residues: 21.6680 Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.097790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070998 restraints weight = 17992.043| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.05 r_work: 0.3042 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2230 Z= 0.171 Angle : 0.658 6.807 3020 Z= 0.341 Chirality : 0.047 0.133 340 Planarity : 0.002 0.007 400 Dihedral : 4.176 9.996 310 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.50 % Allowed : 10.42 % Favored : 87.08 % 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 aren not related in a simple way. whole: -3.98 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.005 0.001 TYR C 37 PHE 0.011 0.002 PHE H 15 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2220) covalent geometry : angle 0.65834 ( 3020) hydrogen bonds : bond 0.05074 ( 101) hydrogen bonds : angle 5.41596 ( 295) Misc. bond : bond 0.00111 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: D 11 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7795 (mmm-85) REVERT: G 11 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7755 (mtm-85) REVERT: H 16 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8563 (tt) REVERT: I 11 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8064 (mtm-85) REVERT: J 11 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7691 (mtm-85) outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 0.6980 time to fit residues: 21.3331 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.073085 restraints weight = 17756.049| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.07 r_work: 0.3081 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2230 Z= 0.100 Angle : 0.556 6.675 3020 Z= 0.281 Chirality : 0.045 0.132 340 Planarity : 0.001 0.007 400 Dihedral : 4.031 9.411 310 Min Nonbonded Distance : 2.700 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.50 % Allowed : 10.00 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 11 TYR 0.004 0.001 TYR C 37 PHE 0.008 0.001 PHE D 15 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 2220) covalent geometry : angle 0.55564 ( 3020) hydrogen bonds : bond 0.03696 ( 101) hydrogen bonds : angle 4.99091 ( 295) Misc. bond : bond 0.00054 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.102 Fit side-chains REVERT: A 11 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6987 (mmt180) REVERT: D 11 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7783 (mmm-85) REVERT: G 11 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: H 16 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8493 (tt) REVERT: I 11 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8102 (mtm-85) REVERT: J 11 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7688 (mtm-85) outliers start: 6 outliers final: 0 residues processed: 29 average time/residue: 0.7411 time to fit residues: 21.9092 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072372 restraints weight = 14600.725| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.92 r_work: 0.3073 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2230 Z= 0.128 Angle : 0.610 7.251 3020 Z= 0.307 Chirality : 0.045 0.130 340 Planarity : 0.002 0.007 400 Dihedral : 4.074 9.551 310 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.67 % Allowed : 10.42 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.95 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.004 0.001 TYR C 37 PHE 0.010 0.001 PHE C 15 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2220) covalent geometry : angle 0.61014 ( 3020) hydrogen bonds : bond 0.04339 ( 101) hydrogen bonds : angle 5.15916 ( 295) Misc. bond : bond 0.00077 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: G 11 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7719 (mtm-85) REVERT: H 16 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8534 (tt) REVERT: I 11 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8069 (mtm-85) REVERT: J 11 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7718 (mtm-85) outliers start: 4 outliers final: 0 residues processed: 28 average time/residue: 0.4082 time to fit residues: 11.6704 Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070469 restraints weight = 17217.195| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.03 r_work: 0.3033 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2230 Z= 0.222 Angle : 0.727 6.890 3020 Z= 0.378 Chirality : 0.049 0.135 340 Planarity : 0.003 0.007 400 Dihedral : 4.203 10.044 310 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.25 % Allowed : 10.83 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.01 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 11 TYR 0.007 0.001 TYR C 37 PHE 0.013 0.002 PHE E 15 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 2220) covalent geometry : angle 0.72653 ( 3020) hydrogen bonds : bond 0.05720 ( 101) hydrogen bonds : angle 5.52688 ( 295) Misc. bond : bond 0.00151 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.051 Fit side-chains revert: symmetry clash REVERT: H 16 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (tt) REVERT: I 11 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8005 (mtm-85) REVERT: J 11 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8232 (mmm-85) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.3703 time to fit residues: 11.3595 Evaluate side-chains 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070915 restraints weight = 18181.871| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.09 r_work: 0.3035 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2230 Z= 0.192 Angle : 0.690 7.111 3020 Z= 0.356 Chirality : 0.048 0.132 340 Planarity : 0.002 0.006 400 Dihedral : 4.173 10.004 310 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % Favored : 87.08 % 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 aren not related in a simple way. whole: -4.01 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.006 0.001 TYR C 37 PHE 0.011 0.002 PHE E 15 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2220) covalent geometry : angle 0.69048 ( 3020) hydrogen bonds : bond 0.05317 ( 101) hydrogen bonds : angle 5.46399 ( 295) Misc. bond : bond 0.00125 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: D 11 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7787 (mmm-85) REVERT: H 16 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8588 (tt) REVERT: I 11 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8004 (mtm-85) REVERT: J 11 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7692 (mtm-85) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.4527 time to fit residues: 14.3181 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074738 restraints weight = 17570.979| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.02 r_work: 0.3105 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 2230 Z= 0.085 Angle : 0.560 7.582 3020 Z= 0.273 Chirality : 0.045 0.133 340 Planarity : 0.001 0.007 400 Dihedral : 3.979 9.457 310 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.25 % Allowed : 12.08 % Favored : 86.67 % 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 aren not related in a simple way. whole: -3.96 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.004 0.001 TYR C 37 PHE 0.008 0.001 PHE C 15 Details of bonding type rmsd covalent geometry : bond 0.00161 ( 2220) covalent geometry : angle 0.56006 ( 3020) hydrogen bonds : bond 0.03133 ( 101) hydrogen bonds : angle 4.85279 ( 295) Misc. bond : bond 0.00034 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.099 Fit side-chains REVERT: D 11 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7728 (mmm-85) REVERT: H 16 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8515 (tt) REVERT: I 11 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8061 (mtm-85) REVERT: J 11 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7710 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 0.7703 time to fit residues: 22.7547 Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.100732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074093 restraints weight = 16387.751| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.98 r_work: 0.3097 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2230 Z= 0.084 Angle : 0.549 7.433 3020 Z= 0.267 Chirality : 0.044 0.132 340 Planarity : 0.001 0.006 400 Dihedral : 3.932 9.268 310 Min Nonbonded Distance : 2.699 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.83 % Allowed : 11.67 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.003 0.001 TYR C 37 PHE 0.008 0.001 PHE D 15 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 2220) covalent geometry : angle 0.54872 ( 3020) hydrogen bonds : bond 0.03163 ( 101) hydrogen bonds : angle 4.78890 ( 295) Misc. bond : bond 0.00040 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.20 seconds wall clock time: 22 minutes 45.62 seconds (1365.62 seconds total)