Starting phenix.real_space_refine on Mon Feb 10 19:46:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbo_61321/02_2025/9jbo_61321_neut.cif" } resolution = 3.39 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1170 2.51 5 N 321 2.21 5 O 375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1872 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 624 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 2.27, per 1000 atoms: 1.21 Number of scatterers: 1872 At special positions: 0 Unit cell: (62.32, 103.36, 35.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 375 8.00 N 321 7.00 C 1170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 265.6 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 438 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 10 Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 23 removed outlier: 6.864A pdb=" N GLN C 15 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY B 16 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLN B 15 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY A 16 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 31 removed outlier: 5.912A pdb=" N LYS C 30 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS B 30 " --> pdb=" O VAL A 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.037A pdb=" N LYS C 36 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR B 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 38 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS B 36 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR A 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 38 " --> pdb=" O THR A 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.495A pdb=" N VAL C 87 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 87 " --> pdb=" O THR A 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.130A pdb=" N SER C 98 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 98 " --> pdb=" O ILE A 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.081A pdb=" N VAL C 103 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 103 " --> pdb=" O ILE A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.900A pdb=" N ILE C 112 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE B 112 " --> pdb=" O ILE A 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 120 24 hydrogen bonds defined for protein. 72 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: 0.43 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 639 1.34 - 1.46: 304 1.46 - 1.58: 944 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 1893 Sorted by residual: bond pdb=" N ILE A 18 " pdb=" CA ILE A 18 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.54e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.45e+00 bond pdb=" N ILE C 18 " pdb=" CA ILE C 18 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.27e+00 bond pdb=" N ASP C 92 " pdb=" CA ASP C 92 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.43e+00 bond pdb=" N ASP B 92 " pdb=" CA ASP B 92 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.37e+00 ... (remaining 1888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 2337 1.26 - 2.52: 181 2.52 - 3.78: 32 3.78 - 5.04: 3 5.04 - 6.31: 3 Bond angle restraints: 2556 Sorted by residual: angle pdb=" CA ASP A 92 " pdb=" CB ASP A 92 " pdb=" CG ASP A 92 " ideal model delta sigma weight residual 112.60 116.20 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA ASP C 92 " pdb=" CB ASP C 92 " pdb=" CG ASP C 92 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 116.19 -3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CA LYS C 91 " pdb=" C LYS C 91 " pdb=" O LYS C 91 " ideal model delta sigma weight residual 121.23 118.20 3.03 1.07e+00 8.73e-01 8.01e+00 angle pdb=" CA LYS B 91 " pdb=" C LYS B 91 " pdb=" O LYS B 91 " ideal model delta sigma weight residual 121.23 118.21 3.02 1.07e+00 8.73e-01 7.96e+00 ... (remaining 2551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 865 12.66 - 25.32: 137 25.32 - 37.98: 63 37.98 - 50.63: 18 50.63 - 63.29: 21 Dihedral angle restraints: 1104 sinusoidal: 414 harmonic: 690 Sorted by residual: dihedral pdb=" CA GLU B 24 " pdb=" CB GLU B 24 " pdb=" CG GLU B 24 " pdb=" CD GLU B 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.33 -57.33 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU C 24 " pdb=" CB GLU C 24 " pdb=" CG GLU C 24 " pdb=" CD GLU C 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.32 -57.32 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU A 24 " pdb=" CB GLU A 24 " pdb=" CG GLU A 24 " pdb=" CD GLU A 24 " ideal model delta sinusoidal sigma weight residual 60.00 117.30 -57.30 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 132 0.024 - 0.047: 78 0.047 - 0.071: 31 0.071 - 0.094: 26 0.094 - 0.118: 39 Chirality restraints: 306 Sorted by residual: chirality pdb=" CA ILE B 113 " pdb=" N ILE B 113 " pdb=" C ILE B 113 " pdb=" CB ILE B 113 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 303 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 32 " -0.005 2.00e-02 2.50e+03 1.55e-02 5.99e+00 pdb=" CG TRP B 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 32 " -0.005 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP C 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP C 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 32 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 32 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 32 " -0.006 2.00e-02 2.50e+03 1.54e-02 5.89e+00 pdb=" CG TRP A 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 32 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 32 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 32 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 32 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 32 " -0.000 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 813 2.94 - 3.43: 1631 3.43 - 3.92: 2943 3.92 - 4.41: 2829 4.41 - 4.90: 5748 Nonbonded interactions: 13964 Sorted by model distance: nonbonded pdb=" ND2 ASN C 19 " pdb=" OD1 ASN B 19 " model vdw 2.444 3.120 nonbonded pdb=" OD1 ASP B 96 " pdb=" N VAL B 97 " model vdw 2.506 3.120 nonbonded pdb=" OD1 ASP C 96 " pdb=" N VAL C 97 " model vdw 2.506 3.120 nonbonded pdb=" OD1 ASP A 96 " pdb=" N VAL A 97 " model vdw 2.506 3.120 nonbonded pdb=" O SER C 25 " pdb=" N ASN B 26 " model vdw 2.507 3.120 ... (remaining 13959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.670 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.005 0.068 1893 Z= 0.348 Angle : 0.760 6.305 2556 Z= 0.474 Chirality : 0.053 0.118 306 Planarity : 0.003 0.023 330 Dihedral : 18.285 63.293 666 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 36.23 % Favored : 63.77 % 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: -3.03 (0.45), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.010 TRP B 32 HIS 0.001 0.000 HIS A 43 PHE 0.007 0.001 PHE C 20 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1630 time to fit residues: 7.2473 Evaluate side-chains 31 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.178036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160596 restraints weight = 3044.162| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.83 r_work: 0.4084 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 1893 Z= 0.274 Angle : 0.685 6.179 2556 Z= 0.357 Chirality : 0.055 0.148 306 Planarity : 0.004 0.038 330 Dihedral : 5.292 15.258 255 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 5.80 % Allowed : 34.78 % Favored : 59.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP C 32 HIS 0.001 0.001 HIS A 110 PHE 0.005 0.001 PHE C 20 ARG 0.001 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.230 Fit side-chains REVERT: C 3 LYS cc_start: 0.7560 (tttt) cc_final: 0.7202 (tttm) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 0.1247 time to fit residues: 6.8710 Evaluate side-chains 38 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.178643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.159662 restraints weight = 3004.612| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.99 r_work: 0.4074 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1893 Z= 0.216 Angle : 0.619 5.668 2556 Z= 0.321 Chirality : 0.054 0.152 306 Planarity : 0.003 0.025 330 Dihedral : 5.225 16.841 255 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 7.25 % Allowed : 32.85 % Favored : 59.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 32 HIS 0.003 0.001 HIS A 120 PHE 0.005 0.001 PHE C 45 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.223 Fit side-chains REVERT: C 3 LYS cc_start: 0.7530 (tttt) cc_final: 0.7179 (tttm) REVERT: A 92 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7427 (t0) outliers start: 15 outliers final: 9 residues processed: 47 average time/residue: 0.1462 time to fit residues: 7.9217 Evaluate side-chains 43 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.177547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159104 restraints weight = 2954.453| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.77 r_work: 0.4078 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1893 Z= 0.226 Angle : 0.625 6.239 2556 Z= 0.323 Chirality : 0.053 0.149 306 Planarity : 0.004 0.030 330 Dihedral : 5.277 16.413 255 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 8.21 % Allowed : 33.33 % Favored : 58.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 32 HIS 0.003 0.001 HIS A 120 PHE 0.004 0.001 PHE C 45 ARG 0.000 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.294 Fit side-chains REVERT: C 3 LYS cc_start: 0.7487 (tttt) cc_final: 0.7146 (tttm) REVERT: B 92 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.6564 (p0) REVERT: A 35 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6431 (mt) REVERT: A 92 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7190 (t70) outliers start: 17 outliers final: 8 residues processed: 46 average time/residue: 0.1228 time to fit residues: 6.6126 Evaluate side-chains 46 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 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 = 0.4413 r_free = 0.4413 target = 0.177768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.158933 restraints weight = 3000.155| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.81 r_work: 0.4081 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1893 Z= 0.227 Angle : 0.634 6.511 2556 Z= 0.327 Chirality : 0.054 0.148 306 Planarity : 0.003 0.025 330 Dihedral : 5.376 17.270 255 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 7.25 % Allowed : 35.27 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 32 HIS 0.003 0.001 HIS A 120 PHE 0.005 0.001 PHE C 45 ARG 0.000 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.234 Fit side-chains REVERT: C 3 LYS cc_start: 0.7509 (tttt) cc_final: 0.7178 (tttm) REVERT: B 92 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.6567 (p0) REVERT: A 92 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6964 (t70) outliers start: 15 outliers final: 11 residues processed: 43 average time/residue: 0.1386 time to fit residues: 7.1149 Evaluate side-chains 45 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4475 r_free = 0.4475 target = 0.183203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.164284 restraints weight = 2986.038| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.83 r_work: 0.4136 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1893 Z= 0.164 Angle : 0.555 5.787 2556 Z= 0.287 Chirality : 0.052 0.144 306 Planarity : 0.003 0.022 330 Dihedral : 4.908 15.335 255 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.31 % Allowed : 36.71 % Favored : 57.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 32 HIS 0.002 0.000 HIS A 120 PHE 0.003 0.001 PHE C 45 ARG 0.000 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.190 Fit side-chains REVERT: C 3 LYS cc_start: 0.7477 (tttt) cc_final: 0.7171 (tttm) REVERT: B 92 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6434 (p0) REVERT: A 92 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6873 (t70) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.1243 time to fit residues: 6.0100 Evaluate side-chains 41 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.177911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.159061 restraints weight = 2910.924| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.78 r_work: 0.4077 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1893 Z= 0.314 Angle : 0.720 7.894 2556 Z= 0.371 Chirality : 0.055 0.145 306 Planarity : 0.004 0.035 330 Dihedral : 5.750 19.057 255 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 7.73 % Allowed : 34.30 % Favored : 57.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 32 HIS 0.004 0.001 HIS A 120 PHE 0.006 0.002 PHE C 45 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.230 Fit side-chains REVERT: C 3 LYS cc_start: 0.7591 (tttt) cc_final: 0.7248 (tttm) REVERT: A 92 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6738 (t70) outliers start: 16 outliers final: 11 residues processed: 43 average time/residue: 0.1243 time to fit residues: 6.3353 Evaluate side-chains 43 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.178996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.159922 restraints weight = 2992.812| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.81 r_work: 0.4081 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1893 Z= 0.275 Angle : 0.685 7.670 2556 Z= 0.351 Chirality : 0.055 0.141 306 Planarity : 0.003 0.024 330 Dihedral : 5.659 18.305 255 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 6.28 % Allowed : 36.23 % Favored : 57.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 32 HIS 0.003 0.001 HIS A 120 PHE 0.006 0.002 PHE C 45 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: C 3 LYS cc_start: 0.7617 (tttt) cc_final: 0.7208 (tttm) REVERT: A 92 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6779 (t70) outliers start: 13 outliers final: 10 residues processed: 42 average time/residue: 0.1259 time to fit residues: 6.2583 Evaluate side-chains 42 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.178939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.159745 restraints weight = 3024.486| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.81 r_work: 0.4078 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1893 Z= 0.283 Angle : 0.700 7.895 2556 Z= 0.358 Chirality : 0.055 0.142 306 Planarity : 0.004 0.030 330 Dihedral : 5.744 18.453 255 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 5.80 % Allowed : 37.20 % Favored : 57.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B 32 HIS 0.003 0.001 HIS A 120 PHE 0.006 0.002 PHE C 45 ARG 0.001 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.233 Fit side-chains REVERT: A 92 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6758 (t70) outliers start: 12 outliers final: 10 residues processed: 43 average time/residue: 0.1307 time to fit residues: 6.6577 Evaluate side-chains 42 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.183065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.163558 restraints weight = 2969.615| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.85 r_work: 0.4117 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1893 Z= 0.188 Angle : 0.619 6.579 2556 Z= 0.315 Chirality : 0.053 0.141 306 Planarity : 0.003 0.020 330 Dihedral : 5.277 17.226 255 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.90 % Allowed : 39.13 % Favored : 57.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 32 HIS 0.002 0.000 HIS A 120 PHE 0.005 0.001 PHE C 45 ARG 0.001 0.000 ARG A 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.227 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.1339 time to fit residues: 6.0190 Evaluate side-chains 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain A residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 overall best weight: 2.6282 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.162611 restraints weight = 2875.145| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.77 r_work: 0.4105 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1893 Z= 0.238 Angle : 0.655 6.972 2556 Z= 0.333 Chirality : 0.054 0.153 306 Planarity : 0.004 0.028 330 Dihedral : 5.415 17.340 255 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 3.38 % Allowed : 39.61 % Favored : 57.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 32 HIS 0.003 0.001 HIS A 120 PHE 0.013 0.002 PHE A 45 ARG 0.001 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.24 seconds wall clock time: 23 minutes 18.17 seconds (1398.17 seconds total)