Starting phenix.real_space_refine on Wed Mar 5 14:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbo_61321/03_2025/9jbo_61321_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbo_61321/03_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_61321/03_2025/9jbo_61321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbo_61321/03_2025/9jbo_61321.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbo_61321/03_2025/9jbo_61321_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbo_61321/03_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-5624/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: 1.90, per 1000 atoms: 1.01 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: 0.42 Conformation dependent library (CDL) restraints added in 240.3 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: 0.28 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: 0.39 Time building geometry restraints manager: 0.51 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: 1.430 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 : 0.220 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1544 time to fit residues: 6.8774 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 : 0.200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 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 = 38)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.160584 restraints weight = 3044.159| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.83 r_work: 0.4089 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.198 Fit side-chains REVERT: C 3 LYS cc_start: 0.7557 (tttt) cc_final: 0.7194 (tttm) outliers start: 12 outliers final: 4 residues processed: 47 average time/residue: 0.1255 time to fit residues: 6.9163 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 : 0.215 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.171442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152440 restraints weight = 2987.281| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.84 r_work: 0.4001 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1893 Z= 0.368 Angle : 0.810 8.075 2556 Z= 0.420 Chirality : 0.058 0.152 306 Planarity : 0.005 0.035 330 Dihedral : 6.377 20.421 255 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 11.11 % Allowed : 32.85 % Favored : 56.04 % 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: -2.70 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 32 HIS 0.005 0.001 HIS A 120 PHE 0.008 0.002 PHE C 45 ARG 0.002 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 56 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.231 Fit side-chains REVERT: C 3 LYS cc_start: 0.7592 (tttt) cc_final: 0.7217 (tttm) REVERT: C 36 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7336 (tttp) REVERT: B 36 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7172 (tttp) REVERT: A 35 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6318 (mt) outliers start: 23 outliers final: 15 residues processed: 48 average time/residue: 0.1510 time to fit residues: 8.3375 Evaluate side-chains 48 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 36 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 42 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 29 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.175629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156877 restraints weight = 2967.774| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.80 r_work: 0.4059 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1893 Z= 0.269 Angle : 0.680 7.376 2556 Z= 0.351 Chirality : 0.055 0.144 306 Planarity : 0.004 0.025 330 Dihedral : 5.768 18.196 255 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 9.66 % Allowed : 34.30 % Favored : 56.04 % 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 0.014 0.004 TRP B 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 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 50 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.225 Fit side-chains REVERT: C 3 LYS cc_start: 0.7582 (tttt) cc_final: 0.7232 (tttm) REVERT: B 92 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.6523 (p0) outliers start: 20 outliers final: 12 residues processed: 44 average time/residue: 0.1380 time to fit residues: 7.0428 Evaluate side-chains 42 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 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 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 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 29 VAL Chi-restraints excluded: chain A residue 42 LEU 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: 8.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.173186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.153740 restraints weight = 2965.060| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.80 r_work: 0.4019 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1893 Z= 0.290 Angle : 0.713 8.085 2556 Z= 0.366 Chirality : 0.056 0.144 306 Planarity : 0.004 0.033 330 Dihedral : 5.885 19.115 255 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 9.66 % Allowed : 32.37 % 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: -2.42 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 32 HIS 0.004 0.001 HIS A 120 PHE 0.006 0.001 PHE C 45 ARG 0.001 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: 20 poor density : 29 time to evaluate : 0.197 Fit side-chains REVERT: C 3 LYS cc_start: 0.7623 (tttt) cc_final: 0.7259 (tttm) outliers start: 20 outliers final: 13 residues processed: 43 average time/residue: 0.1285 time to fit residues: 6.4902 Evaluate side-chains 41 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 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 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 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.0070 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.184250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.165308 restraints weight = 2991.012| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.79 r_work: 0.4151 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1893 Z= 0.143 Angle : 0.534 4.811 2556 Z= 0.277 Chirality : 0.052 0.144 306 Planarity : 0.002 0.014 330 Dihedral : 4.843 15.695 255 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.86 % Allowed : 37.20 % Favored : 58.94 % 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: -2.20 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 32 HIS 0.001 0.000 HIS A 120 PHE 0.004 0.001 PHE A 20 ARG 0.001 0.000 ARG C 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 40 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.217 Fit side-chains REVERT: B 92 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.6425 (p0) outliers start: 8 outliers final: 4 residues processed: 38 average time/residue: 0.1229 time to fit residues: 5.5797 Evaluate side-chains 34 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 38 LEU 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: 8.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.181379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.162935 restraints weight = 2897.314| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.67 r_work: 0.4109 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1893 Z= 0.246 Angle : 0.627 6.876 2556 Z= 0.322 Chirality : 0.053 0.155 306 Planarity : 0.004 0.032 330 Dihedral : 5.185 15.947 255 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.86 % Allowed : 39.13 % 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 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 32 HIS 0.003 0.001 HIS A 120 PHE 0.021 0.002 PHE A 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 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.213 Fit side-chains REVERT: A 90 ASP cc_start: 0.5263 (t0) cc_final: 0.4751 (p0) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1220 time to fit residues: 4.9847 Evaluate side-chains 35 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.186662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.167801 restraints weight = 2985.371| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.71 r_work: 0.4172 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1893 Z= 0.138 Angle : 0.532 5.677 2556 Z= 0.272 Chirality : 0.051 0.152 306 Planarity : 0.002 0.016 330 Dihedral : 4.717 14.699 255 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.93 % Allowed : 40.10 % 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 : -1.55 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 32 HIS 0.002 0.000 HIS A 120 PHE 0.015 0.001 PHE A 45 ARG 0.000 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 36 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.204 Fit side-chains REVERT: A 90 ASP cc_start: 0.5225 (t0) cc_final: 0.4651 (t0) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1344 time to fit residues: 5.4250 Evaluate side-chains 34 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.4445 r_free = 0.4445 target = 0.179736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.161047 restraints weight = 3020.437| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.75 r_work: 0.4091 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1893 Z= 0.301 Angle : 0.683 7.331 2556 Z= 0.349 Chirality : 0.055 0.153 306 Planarity : 0.004 0.038 330 Dihedral : 5.487 18.159 255 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 3.86 % Allowed : 39.13 % 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: -2.16 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 32 HIS 0.004 0.001 HIS A 120 PHE 0.007 0.002 PHE A 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 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.215 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 35 average time/residue: 0.1185 time to fit residues: 4.9835 Evaluate side-chains 33 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 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 A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.0170 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.181441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.162910 restraints weight = 3010.570| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.70 r_work: 0.4106 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1893 Z= 0.230 Angle : 0.649 7.134 2556 Z= 0.330 Chirality : 0.054 0.152 306 Planarity : 0.003 0.021 330 Dihedral : 5.416 17.994 255 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 3.86 % Allowed : 39.13 % 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: -2.10 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 32 HIS 0.003 0.001 HIS A 120 PHE 0.005 0.001 PHE A 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 37 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.231 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1227 time to fit residues: 5.0095 Evaluate side-chains 34 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.173499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154399 restraints weight = 2917.316| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.74 r_work: 0.4029 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 1893 Z= 0.345 Angle : 0.763 8.450 2556 Z= 0.389 Chirality : 0.057 0.154 306 Planarity : 0.005 0.038 330 Dihedral : 5.993 19.600 255 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 4.35 % Allowed : 38.16 % 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: -2.23 (0.47), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 32 HIS 0.005 0.001 HIS A 120 PHE 0.006 0.002 PHE B 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: 1271.90 seconds wall clock time: 22 minutes 47.27 seconds (1367.27 seconds total)