Starting phenix.real_space_refine on Wed Jul 23 08:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az4_15753/07_2025/8az4_15753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az4_15753/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8az4_15753/07_2025/8az4_15753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az4_15753/07_2025/8az4_15753.map" model { file = "/net/cci-nas-00/data/ceres_data/8az4_15753/07_2025/8az4_15753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az4_15753/07_2025/8az4_15753.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.21, per 1000 atoms: 1.41 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: 0.58 Conformation dependent library (CDL) restraints added in 481.2 milliseconds 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: 0.33 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: 0.54 Time building geometry restraints manager: 0.69 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.090 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.380 Find NCS groups from input model: 0.060 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (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 PHE 0.013 0.002 PHE E 15 TYR 0.010 0.002 TYR E 37 ARG 0.002 0.001 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.15728 ( 101) hydrogen bonds : angle 7.13756 ( 295) covalent geometry : bond 0.00624 ( 2220) covalent geometry : angle 0.72032 ( 3020) 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 : 0.406 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: 1.3138 time to fit residues: 44.5180 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.098576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071438 restraints weight = 16143.312| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.02 r_work: 0.3053 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 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 = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1674 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= 0.135 Angle : 0.620 5.914 3020 Z= 0.324 Chirality : 0.047 0.135 340 Planarity : 0.002 0.013 400 Dihedral : 4.232 10.368 310 Min Nonbonded Distance : 2.683 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (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 PHE 0.010 0.002 PHE H 15 TYR 0.004 0.001 TYR I 37 ARG 0.003 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 101) hydrogen bonds : angle 5.38724 ( 295) covalent geometry : bond 0.00273 ( 2220) covalent geometry : angle 0.61960 ( 3020) Misc. bond : bond 0.00081 ( 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 : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7655 (mtm-85) REVERT: I 11 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8059 (mtm-85) REVERT: J 11 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.7690 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 1.0370 time to fit residues: 35.2087 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 : 0.259 ------------------------------------------------------------------------------- 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 6 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.098738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071255 restraints weight = 20913.887| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.21 r_work: 0.3042 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 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 = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2230 Z= 0.144 Angle : 0.629 6.550 3020 Z= 0.325 Chirality : 0.047 0.135 340 Planarity : 0.002 0.008 400 Dihedral : 4.132 10.190 310 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.50 % Allowed : 8.33 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 15 TYR 0.003 0.001 TYR C 37 ARG 0.003 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 101) hydrogen bonds : angle 5.34762 ( 295) covalent geometry : bond 0.00299 ( 2220) covalent geometry : angle 0.62903 ( 3020) Misc. bond : bond 0.00085 ( 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 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8069 (mmm-85) REVERT: D 11 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7762 (mmm-85) REVERT: G 11 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7764 (mtm-85) REVERT: H 16 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8516 (tt) REVERT: I 11 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8109 (mtm-85) REVERT: J 11 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7719 (mtm-85) outliers start: 6 outliers final: 0 residues processed: 28 average time/residue: 1.3486 time to fit residues: 38.6412 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 : 0.229 ------------------------------------------------------------------------------- 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 7 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.097880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.071027 restraints weight = 20735.695| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.11 r_work: 0.3034 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 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 = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1827 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= 0.162 Angle : 0.632 6.526 3020 Z= 0.331 Chirality : 0.047 0.134 340 Planarity : 0.002 0.007 400 Dihedral : 4.163 10.191 310 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.29), 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 PHE 0.011 0.002 PHE C 15 TYR 0.004 0.001 TYR C 37 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 101) hydrogen bonds : angle 5.39008 ( 295) covalent geometry : bond 0.00344 ( 2220) covalent geometry : angle 0.63238 ( 3020) Misc. bond : bond 0.00105 ( 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 : 0.267 Fit side-chains revert: symmetry clash REVERT: G 11 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7779 (mtm-85) REVERT: H 16 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8576 (tt) REVERT: I 11 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8083 (mtm-85) REVERT: J 11 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7721 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.3341 time to fit residues: 39.6121 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 : 0.225 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 2.5724 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.098588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071307 restraints weight = 14870.026| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.99 r_work: 0.3050 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2230 Z= 0.160 Angle : 0.635 6.729 3020 Z= 0.331 Chirality : 0.047 0.133 340 Planarity : 0.002 0.008 400 Dihedral : 4.141 9.969 310 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 1.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (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 PHE 0.010 0.002 PHE H 15 TYR 0.005 0.001 TYR C 37 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 101) hydrogen bonds : angle 5.36178 ( 295) covalent geometry : bond 0.00339 ( 2220) covalent geometry : angle 0.63477 ( 3020) Misc. bond : bond 0.00102 ( 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 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.325 Fit side-chains REVERT: A 11 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7044 (mmt180) REVERT: G 11 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7744 (mtm-85) REVERT: H 16 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8547 (tt) REVERT: I 11 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8067 (mtm-85) REVERT: J 11 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7713 (mtm-85) outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 1.3966 time to fit residues: 42.9165 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 : 0.258 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.097219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070300 restraints weight = 17067.748| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.05 r_work: 0.3027 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 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 = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2230 Z= 0.225 Angle : 0.712 6.248 3020 Z= 0.377 Chirality : 0.049 0.135 340 Planarity : 0.003 0.007 400 Dihedral : 4.223 10.069 310 Min Nonbonded Distance : 2.646 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 15 TYR 0.007 0.001 TYR C 37 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.05758 ( 101) hydrogen bonds : angle 5.55464 ( 295) covalent geometry : bond 0.00486 ( 2220) covalent geometry : angle 0.71230 ( 3020) Misc. bond : bond 0.00149 ( 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 35 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: D 11 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7781 (mmm-85) REVERT: H 16 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8572 (tt) REVERT: I 11 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8002 (mtm-85) REVERT: J 11 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7685 (mtm-85) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 1.2761 time to fit residues: 40.5165 Evaluate side-chains 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.097633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070541 restraints weight = 14709.705| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.98 r_work: 0.3036 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 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 = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2230 Z= 0.224 Angle : 0.729 6.726 3020 Z= 0.379 Chirality : 0.049 0.136 340 Planarity : 0.003 0.008 400 Dihedral : 4.210 10.077 310 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.007 0.001 TYR C 37 ARG 0.002 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.05712 ( 101) hydrogen bonds : angle 5.53480 ( 295) covalent geometry : bond 0.00484 ( 2220) covalent geometry : angle 0.72924 ( 3020) Misc. bond : bond 0.00148 ( 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 34 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: D 11 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7760 (mmm-85) REVERT: F 12 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8569 (tp) REVERT: H 16 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (tt) REVERT: I 11 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8010 (mtm-85) REVERT: J 11 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8192 (mmm-85) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 1.2827 time to fit residues: 40.7339 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 : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain F residue 12 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072540 restraints weight = 19378.164| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.08 r_work: 0.3064 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1994 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= 0.116 Angle : 0.587 7.223 3020 Z= 0.298 Chirality : 0.045 0.132 340 Planarity : 0.002 0.007 400 Dihedral : 4.060 9.511 310 Min Nonbonded Distance : 2.699 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.25 % Allowed : 11.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 101) hydrogen bonds : angle 5.12491 ( 295) covalent geometry : bond 0.00236 ( 2220) covalent geometry : angle 0.58738 ( 3020) Misc. bond : bond 0.00064 ( 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 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.243 Fit side-chains REVERT: D 11 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7739 (mmm-85) REVERT: H 16 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8532 (tt) REVERT: I 11 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8012 (mtm-85) REVERT: J 11 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7691 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 1.3547 time to fit residues: 40.1858 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 : 0.266 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.100281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073745 restraints weight = 13886.498| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.88 r_work: 0.3094 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2230 Z= 0.093 Angle : 0.569 7.380 3020 Z= 0.278 Chirality : 0.045 0.132 340 Planarity : 0.001 0.006 400 Dihedral : 3.983 9.391 310 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (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 PHE 0.008 0.001 PHE D 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 101) hydrogen bonds : angle 4.88078 ( 295) covalent geometry : bond 0.00181 ( 2220) covalent geometry : angle 0.56861 ( 3020) Misc. bond : bond 0.00045 ( 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 32 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.256 Fit side-chains REVERT: D 11 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7754 (mmm-85) REVERT: G 11 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7718 (mtm-85) REVERT: H 16 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8459 (tt) REVERT: I 11 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8110 (mtm-85) REVERT: J 11 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7703 (mtm-85) outliers start: 4 outliers final: 0 residues processed: 29 average time/residue: 1.3561 time to fit residues: 40.2311 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 : 0.231 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.100722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074032 restraints weight = 18113.127| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.05 r_work: 0.3095 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2200 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= 0.085 Angle : 0.540 7.441 3020 Z= 0.266 Chirality : 0.044 0.132 340 Planarity : 0.001 0.005 400 Dihedral : 3.950 9.322 310 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.08 % Allowed : 10.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 15 TYR 0.003 0.001 TYR C 37 ARG 0.001 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 101) hydrogen bonds : angle 4.78293 ( 295) covalent geometry : bond 0.00165 ( 2220) covalent geometry : angle 0.54045 ( 3020) Misc. bond : bond 0.00042 ( 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 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.257 Fit side-chains REVERT: D 11 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7745 (mmm-85) REVERT: G 11 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7723 (mtm-85) REVERT: H 16 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8470 (tt) REVERT: I 11 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8103 (mtm-85) REVERT: J 11 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7694 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 30 average time/residue: 1.3328 time to fit residues: 40.9246 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 : 0.235 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.099106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072277 restraints weight = 16300.256| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.99 r_work: 0.3068 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 2230 Z= 0.130 Angle : 0.626 7.163 3020 Z= 0.310 Chirality : 0.045 0.130 340 Planarity : 0.002 0.005 400 Dihedral : 4.057 9.293 310 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.25 % Allowed : 11.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (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 PHE 0.010 0.002 PHE C 15 TYR 0.005 0.001 TYR C 37 ARG 0.002 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 101) hydrogen bonds : angle 5.12794 ( 295) covalent geometry : bond 0.00270 ( 2220) covalent geometry : angle 0.62620 ( 3020) Misc. bond : bond 0.00078 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.42 seconds wall clock time: 46 minutes 8.82 seconds (2768.82 seconds total)