Starting phenix.real_space_refine on Mon Feb 10 20:28:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az4_15753/02_2025/8az4_15753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az4_15753/02_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_15753/02_2025/8az4_15753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az4_15753/02_2025/8az4_15753.map" model { file = "/net/cci-nas-00/data/ceres_data/8az4_15753/02_2025/8az4_15753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az4_15753/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.05, per 1000 atoms: 1.34 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: 0.61 Conformation dependent library (CDL) restraints added in 507.5 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: 0.34 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: 0.60 Time building geometry restraints manager: 0.70 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: 1.170 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- 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 : 0.006 0.029 2220 Z= 0.418 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 *********************** 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 : 0.252 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: 1.3422 time to fit residues: 45.2894 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 : 0.265 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 21 ASN I 18 HIS A I 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070942 restraints weight = 16160.777| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.00 r_work: 0.3046 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2220 Z= 0.228 Angle : 0.662 5.880 3020 Z= 0.348 Chirality : 0.049 0.137 340 Planarity : 0.002 0.012 400 Dihedral : 4.272 10.504 310 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -3.77 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.003 0.001 TYR A 37 ARG 0.003 0.000 ARG C 11 *********************** 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 : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7962 (mmm-85) REVERT: I 11 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8053 (mtm-85) REVERT: J 11 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.7683 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 1.1954 time to fit residues: 40.4254 Evaluate side-chains 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS A I 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072458 restraints weight = 20803.199| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.15 r_work: 0.3060 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2220 Z= 0.144 Angle : 0.576 6.764 3020 Z= 0.292 Chirality : 0.045 0.133 340 Planarity : 0.002 0.011 400 Dihedral : 4.076 9.755 310 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.67 % Allowed : 9.58 % 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: -3.85 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 15 TYR 0.003 0.001 TYR C 37 ARG 0.003 0.000 ARG C 11 *********************** 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 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (mmm-85) REVERT: I 11 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8092 (mtm-85) REVERT: J 11 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7715 (mtm-85) outliers start: 4 outliers final: 0 residues processed: 27 average time/residue: 1.3252 time to fit residues: 36.7063 Evaluate side-chains 29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG 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: 6.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 0.0010 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.099014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071931 restraints weight = 20686.204| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.16 r_work: 0.3053 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2220 Z= 0.169 Angle : 0.592 7.087 3020 Z= 0.301 Chirality : 0.045 0.132 340 Planarity : 0.002 0.007 400 Dihedral : 4.082 9.764 310 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.50 % Allowed : 8.75 % 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: -3.91 (0.30), 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 PHE 0.009 0.001 PHE C 15 TYR 0.003 0.001 TYR C 37 ARG 0.003 0.000 ARG C 11 *********************** 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 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.342 Fit side-chains REVERT: A 11 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8017 (mmm-85) REVERT: D 11 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7795 (mmm-85) REVERT: G 11 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7734 (mtm-85) REVERT: I 11 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8155 (mtm-85) REVERT: J 11 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7715 (mtm-85) outliers start: 6 outliers final: 0 residues processed: 28 average time/residue: 1.4737 time to fit residues: 42.2071 Evaluate side-chains 31 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.0030 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072901 restraints weight = 14791.204| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.91 r_work: 0.3078 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2220 Z= 0.150 Angle : 0.560 6.947 3020 Z= 0.287 Chirality : 0.045 0.132 340 Planarity : 0.002 0.004 400 Dihedral : 4.037 9.589 310 Min Nonbonded Distance : 2.703 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.25 % Allowed : 10.00 % 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: -3.93 (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 0.009 0.001 PHE C 15 TYR 0.003 0.001 TYR C 37 ARG 0.001 0.000 ARG F 11 *********************** 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 30 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.271 Fit side-chains REVERT: G 11 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7682 (mtm-85) REVERT: I 11 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8136 (mtm-85) REVERT: J 11 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7689 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 27 average time/residue: 1.3331 time to fit residues: 36.8926 Evaluate side-chains 29 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 18 HIS A Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073538 restraints weight = 17050.194| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.02 r_work: 0.3092 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2220 Z= 0.122 Angle : 0.548 6.967 3020 Z= 0.273 Chirality : 0.044 0.130 340 Planarity : 0.001 0.005 400 Dihedral : 3.984 9.189 310 Min Nonbonded Distance : 2.700 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.25 % Allowed : 10.00 % 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: -3.91 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (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 *********************** 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 30 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.244 Fit side-chains REVERT: A 11 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7927 (mmm-85) REVERT: G 11 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: I 11 ARG cc_start: 0.8601 (mtt180) cc_final: 0.8142 (mtm-85) REVERT: J 11 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7706 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 27 average time/residue: 1.3144 time to fit residues: 36.3893 Evaluate side-chains 30 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG 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 8 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.097315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070301 restraints weight = 14696.727| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.95 r_work: 0.3037 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 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 = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2220 Z= 0.386 Angle : 0.761 6.561 3020 Z= 0.396 Chirality : 0.050 0.138 340 Planarity : 0.003 0.008 400 Dihedral : 4.232 10.277 310 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.50 % Allowed : 8.75 % 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: -3.98 (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 PHE 0.014 0.002 PHE H 15 TYR 0.007 0.001 TYR C 37 ARG 0.001 0.000 ARG B 11 *********************** 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 36 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: D 11 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7768 (mmm-85) REVERT: G 11 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7759 (mtm-85) REVERT: H 16 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8609 (tt) REVERT: I 11 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8070 (mtm-85) REVERT: J 11 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8230 (mmm-85) outliers start: 6 outliers final: 1 residues processed: 31 average time/residue: 1.3915 time to fit residues: 44.1777 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 : 0.289 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072794 restraints weight = 19329.806| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.08 r_work: 0.3069 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2220 Z= 0.154 Angle : 0.592 7.251 3020 Z= 0.298 Chirality : 0.045 0.130 340 Planarity : 0.002 0.007 400 Dihedral : 4.048 9.427 310 Min Nonbonded Distance : 2.699 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.08 % Allowed : 9.17 % 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: -3.97 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), 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 *********************** 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 33 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.262 Fit side-chains REVERT: A 11 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7000 (mmt180) REVERT: D 11 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7738 (mmm-85) REVERT: G 11 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7692 (mtm-85) REVERT: H 16 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8532 (tt) REVERT: I 11 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8127 (mtm-85) REVERT: J 11 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7711 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.4579 time to fit residues: 43.2282 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 ------------------------------------------------------------------------------- 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=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: 9.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.098899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071686 restraints weight = 13923.865| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.93 r_work: 0.3064 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 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 = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2220 Z= 0.226 Angle : 0.657 7.024 3020 Z= 0.331 Chirality : 0.046 0.134 340 Planarity : 0.002 0.005 400 Dihedral : 4.103 9.741 310 Min Nonbonded Distance : 2.682 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: -3.97 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE E 15 TYR 0.005 0.001 TYR C 37 ARG 0.002 0.000 ARG A 11 *********************** 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: 5 poor density : 28 time to evaluate : 0.253 Fit side-chains REVERT: A 11 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7005 (mmt180) REVERT: D 11 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7749 (mmm-85) REVERT: G 11 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7715 (mtm-85) REVERT: H 16 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8569 (tt) REVERT: I 11 ARG cc_start: 0.8617 (mtt180) cc_final: 0.8072 (mtm-85) REVERT: J 11 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7709 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.4415 time to fit residues: 42.7428 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 : 0.262 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.099606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072654 restraints weight = 18096.458| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.07 r_work: 0.3070 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2220 Z= 0.164 Angle : 0.601 7.295 3020 Z= 0.301 Chirality : 0.045 0.131 340 Planarity : 0.002 0.005 400 Dihedral : 4.053 9.620 310 Min Nonbonded Distance : 2.700 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % 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: -3.98 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 15 TYR 0.004 0.001 TYR C 37 ARG 0.001 0.000 ARG A 11 ********************** 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 : 0.239 Fit side-chains REVERT: D 11 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7743 (mmm-85) REVERT: G 11 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: H 16 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (tt) REVERT: I 11 ARG cc_start: 0.8622 (mtt180) cc_final: 0.8128 (mtm-85) REVERT: J 11 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7685 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.4606 time to fit residues: 43.3449 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 : 0.243 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.100120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073409 restraints weight = 16280.689| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.99 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2220 Z= 0.138 Angle : 0.585 7.411 3020 Z= 0.286 Chirality : 0.045 0.131 340 Planarity : 0.001 0.006 400 Dihedral : 4.010 9.282 310 Min Nonbonded Distance : 2.699 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.67 % Allowed : 10.83 % 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 E 15 TYR 0.003 0.001 TYR C 37 ARG 0.001 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.59 seconds wall clock time: 45 minutes 59.51 seconds (2759.51 seconds total)