Starting phenix.real_space_refine on Mon Feb 10 19:27:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf5_37199/02_2025/8kf5_37199.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 978 2.51 5 N 252 2.21 5 O 264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 0.99, per 1000 atoms: 0.66 Number of scatterers: 1500 At special positions: 0 Unit cell: (67.23, 69.72, 35.69, 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 264 8.00 N 252 7.00 C 978 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: 1.13 Conformation dependent library (CDL) restraints added in 200.5 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'D' and resid 16 through 17 removed outlier: 6.648A pdb=" N LYS D 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS E 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 30 through 36 removed outlier: 8.801A pdb=" N ILE D 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N LEU E 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY D 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL E 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET D 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ILE E 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N LEU F 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY E 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VAL F 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET E 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.226A pdb=" N VAL D 40 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL E 40 " --> pdb=" O ILE F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 16 through 17 removed outlier: 6.649A pdb=" N LYS C 16 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS A 16 " --> pdb=" O LEU B 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 36 removed outlier: 8.815A pdb=" N ILE C 31 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N LEU A 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C 33 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL A 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET C 35 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N LEU B 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY A 33 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL B 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET A 35 " --> pdb=" O VAL B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.219A pdb=" N VAL C 40 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 40 " --> pdb=" O ILE B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 4 hydrogen bonds defined for protein. 12 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: 0.31 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 486 1.34 - 1.45: 180 1.45 - 1.56: 846 1.56 - 1.67: 0 1.67 - 1.79: 12 Bond restraints: 1524 Sorted by residual: bond pdb=" CG LEU F 34 " pdb=" CD1 LEU F 34 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG LEU A 34 " pdb=" CD1 LEU A 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CG LEU D 34 " pdb=" CD1 LEU D 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CG LEU B 34 " pdb=" CD1 LEU B 34 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 ... (remaining 1519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 1596 0.86 - 1.72: 337 1.72 - 2.58: 89 2.58 - 3.44: 18 3.44 - 4.30: 6 Bond angle restraints: 2046 Sorted by residual: angle pdb=" N GLU F 11 " pdb=" CA GLU F 11 " pdb=" C GLU F 11 " ideal model delta sigma weight residual 107.49 111.79 -4.30 1.74e+00 3.30e-01 6.11e+00 angle pdb=" N GLU D 11 " pdb=" CA GLU D 11 " pdb=" C GLU D 11 " ideal model delta sigma weight residual 107.49 111.78 -4.29 1.74e+00 3.30e-01 6.08e+00 angle pdb=" N GLU C 11 " pdb=" CA GLU C 11 " pdb=" C GLU C 11 " ideal model delta sigma weight residual 107.49 111.78 -4.29 1.74e+00 3.30e-01 6.07e+00 angle pdb=" N GLU E 11 " pdb=" CA GLU E 11 " pdb=" C GLU E 11 " ideal model delta sigma weight residual 107.49 111.77 -4.28 1.74e+00 3.30e-01 6.05e+00 angle pdb=" N GLU A 11 " pdb=" CA GLU A 11 " pdb=" C GLU A 11 " ideal model delta sigma weight residual 107.49 111.76 -4.27 1.74e+00 3.30e-01 6.03e+00 ... (remaining 2041 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.76: 684 11.76 - 23.51: 100 23.51 - 35.27: 32 35.27 - 47.02: 24 47.02 - 58.78: 6 Dihedral angle restraints: 846 sinusoidal: 306 harmonic: 540 Sorted by residual: dihedral pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " ideal model delta sinusoidal sigma weight residual -60.00 -104.55 44.55 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" CB GLU D 22 " pdb=" CG GLU D 22 " ideal model delta sinusoidal sigma weight residual -60.00 -104.52 44.52 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" CB GLU E 22 " pdb=" CG GLU E 22 " ideal model delta sinusoidal sigma weight residual -60.00 -104.49 44.49 3 1.50e+01 4.44e-03 8.00e+00 ... (remaining 843 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.035: 101 0.035 - 0.069: 55 0.069 - 0.103: 30 0.103 - 0.137: 24 0.137 - 0.171: 24 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA VAL C 24 " pdb=" N VAL C 24 " pdb=" C VAL C 24 " pdb=" CB VAL C 24 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA VAL F 24 " pdb=" N VAL F 24 " pdb=" C VAL F 24 " pdb=" CB VAL F 24 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 231 not shown) Planarity restraints: 258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 20 " 0.006 2.00e-02 2.50e+03 4.61e-03 3.71e-01 pdb=" CG PHE F 20 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE F 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 20 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 14 " 0.005 2.00e-02 2.50e+03 4.90e-03 3.60e-01 pdb=" CG HIS A 14 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 14 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 14 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 14 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 20 " 0.006 2.00e-02 2.50e+03 4.53e-03 3.59e-01 pdb=" CG PHE E 20 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE E 20 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 20 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 20 " 0.001 2.00e-02 2.50e+03 ... (remaining 255 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 589 2.85 - 3.37: 1186 3.37 - 3.88: 2433 3.88 - 4.39: 2446 4.39 - 4.90: 4976 Nonbonded interactions: 11630 Sorted by model distance: nonbonded pdb=" CB GLU E 22 " pdb=" N ASP F 23 " model vdw 2.343 3.520 nonbonded pdb=" CB GLU A 22 " pdb=" N ASP B 23 " model vdw 2.346 3.520 nonbonded pdb=" CB GLU D 22 " pdb=" N ASP E 23 " model vdw 2.354 3.520 nonbonded pdb=" CB GLU C 22 " pdb=" N ASP A 23 " model vdw 2.367 3.520 nonbonded pdb=" OD1 ASN B 27 " pdb=" N LYS B 28 " model vdw 2.386 3.120 ... (remaining 11625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 1524 Z= 0.655 Angle : 0.826 4.301 2046 Z= 0.519 Chirality : 0.076 0.171 234 Planarity : 0.003 0.006 258 Dihedral : 15.442 58.776 510 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 8.00 % Allowed : 4.00 % Favored : 88.00 % 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: -3.84 (0.39), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 14 PHE 0.010 0.002 PHE F 20 TYR 0.001 0.000 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.172 Fit side-chains REVERT: D 28 LYS cc_start: 0.8628 (mttt) cc_final: 0.8405 (mttp) REVERT: F 22 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: B 22 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.6746 (pt0) outliers start: 12 outliers final: 6 residues processed: 30 average time/residue: 0.1774 time to fit residues: 5.9563 Evaluate side-chains 26 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.117110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095301 restraints weight = 1940.372| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.81 r_work: 0.3464 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1524 Z= 0.161 Angle : 0.502 3.538 2046 Z= 0.292 Chirality : 0.060 0.124 234 Planarity : 0.002 0.007 258 Dihedral : 8.717 44.414 224 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.45 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 13 PHE 0.003 0.001 PHE C 20 TYR 0.006 0.001 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.172 Fit side-chains REVERT: C 14 HIS cc_start: 0.8459 (m90) cc_final: 0.8196 (m90) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1727 time to fit residues: 5.6971 Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.112432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089789 restraints weight = 1918.478| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.67 r_work: 0.3362 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 1524 Z= 0.397 Angle : 0.577 4.315 2046 Z= 0.328 Chirality : 0.063 0.142 234 Planarity : 0.002 0.006 258 Dihedral : 4.708 13.558 204 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % 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: -1.65 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 14 PHE 0.009 0.002 PHE E 20 TYR 0.006 0.001 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.223 Fit side-chains REVERT: D 22 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8424 (tp30) REVERT: B 10 TYR cc_start: 0.8746 (m-80) cc_final: 0.8469 (m-80) REVERT: B 23 ASP cc_start: 0.8427 (p0) cc_final: 0.8166 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1929 time to fit residues: 5.2382 Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.116096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092607 restraints weight = 1880.256| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.80 r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1524 Z= 0.146 Angle : 0.461 3.238 2046 Z= 0.263 Chirality : 0.059 0.125 234 Planarity : 0.001 0.004 258 Dihedral : 4.111 12.133 204 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 13 PHE 0.003 0.001 PHE A 20 TYR 0.009 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.168 Fit side-chains REVERT: D 22 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8224 (tp30) REVERT: F 23 ASP cc_start: 0.8318 (p0) cc_final: 0.8082 (p0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1958 time to fit residues: 5.0544 Evaluate side-chains 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.108518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.084835 restraints weight = 1932.367| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.78 r_work: 0.3288 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 1524 Z= 0.405 Angle : 0.573 4.331 2046 Z= 0.321 Chirality : 0.061 0.134 234 Planarity : 0.002 0.011 258 Dihedral : 4.646 13.710 204 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.53), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 13 PHE 0.012 0.002 PHE B 20 TYR 0.008 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.165 Fit side-chains REVERT: D 22 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8392 (tp30) REVERT: A 23 ASP cc_start: 0.8288 (p0) cc_final: 0.7973 (p0) REVERT: F 23 ASP cc_start: 0.8298 (p0) cc_final: 0.8051 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1866 time to fit residues: 5.2399 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.111540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.087909 restraints weight = 1981.621| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.81 r_work: 0.3349 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1524 Z= 0.267 Angle : 0.521 4.123 2046 Z= 0.292 Chirality : 0.060 0.128 234 Planarity : 0.001 0.006 258 Dihedral : 4.389 12.569 204 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 13 PHE 0.008 0.001 PHE B 20 TYR 0.009 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.166 Fit side-chains REVERT: D 22 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8379 (tp30) REVERT: F 23 ASP cc_start: 0.8301 (p0) cc_final: 0.8064 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1913 time to fit residues: 5.3593 Evaluate side-chains 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.0030 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.109908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086065 restraints weight = 1952.505| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.73 r_work: 0.3302 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1524 Z= 0.360 Angle : 0.569 4.533 2046 Z= 0.318 Chirality : 0.061 0.131 234 Planarity : 0.002 0.012 258 Dihedral : 4.609 13.729 204 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 13 PHE 0.011 0.002 PHE B 20 TYR 0.008 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.169 Fit side-chains REVERT: D 22 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8390 (tp30) REVERT: F 23 ASP cc_start: 0.8290 (p0) cc_final: 0.8086 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1998 time to fit residues: 5.4054 Evaluate side-chains 24 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.113864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090191 restraints weight = 1905.412| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.72 r_work: 0.3366 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1524 Z= 0.221 Angle : 0.513 4.226 2046 Z= 0.287 Chirality : 0.060 0.127 234 Planarity : 0.002 0.011 258 Dihedral : 4.277 11.931 204 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.58), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.20 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 13 PHE 0.006 0.001 PHE B 20 TYR 0.009 0.002 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2031 time to fit residues: 5.0184 Evaluate side-chains 22 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089824 restraints weight = 1910.633| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.76 r_work: 0.3370 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1524 Z= 0.232 Angle : 0.516 4.057 2046 Z= 0.290 Chirality : 0.060 0.125 234 Planarity : 0.002 0.010 258 Dihedral : 4.214 11.823 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.60), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.12 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 13 PHE 0.006 0.001 PHE B 20 TYR 0.009 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.158 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2080 time to fit residues: 4.8912 Evaluate side-chains 20 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.118214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.093262 restraints weight = 1876.307| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.89 r_work: 0.3446 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1524 Z= 0.146 Angle : 0.464 3.792 2046 Z= 0.262 Chirality : 0.058 0.121 234 Planarity : 0.001 0.010 258 Dihedral : 3.913 11.599 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.61), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.06 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 13 PHE 0.003 0.001 PHE B 20 TYR 0.008 0.002 TYR C 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2111 time to fit residues: 4.5191 Evaluate side-chains 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.118093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093413 restraints weight = 1940.641| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.83 r_work: 0.3437 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1524 Z= 0.177 Angle : 0.473 3.753 2046 Z= 0.267 Chirality : 0.058 0.123 234 Planarity : 0.001 0.010 258 Dihedral : 3.899 11.264 204 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % 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: -0.04 (0.61), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.02 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.004 0.001 PHE B 20 TYR 0.010 0.001 TYR C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.06 seconds wall clock time: 23 minutes 53.92 seconds (1433.92 seconds total)