Starting phenix.real_space_refine on Fri Aug 22 12:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf5_37199/08_2025/8kf5_37199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf5_37199/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kf5_37199/08_2025/8kf5_37199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf5_37199/08_2025/8kf5_37199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kf5_37199/08_2025/8kf5_37199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf5_37199/08_2025/8kf5_37199.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" 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, E, A, F, B Time building chain proxies: 0.35, per 1000 atoms: 0.23 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: 0.11 Conformation dependent library (CDL) restraints added in 41.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.04 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: 0.09 Time building geometry restraints manager: 0.11 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: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'C' selection = chain 'E' selection = chain 'A' selection = chain 'F' 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: 1.510 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.400 Find NCS groups from input model: 0.010 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:0.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.680 ------------------------------------------------------------------------------- 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= 0.408 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.001 0.000 TYR C 10 PHE 0.010 0.002 PHE F 20 HIS 0.005 0.002 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 1524) covalent geometry : angle 0.82575 ( 2046) hydrogen bonds : bond 0.24358 ( 4) hydrogen bonds : angle 9.75139 ( 12) *********************** 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 : 0.033 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: 0.0484 time to fit residues: 1.6248 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 : 0.032 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.116656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094741 restraints weight = 1959.312| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.81 r_work: 0.3476 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1524 Z= 0.092 Angle : 0.504 3.573 2046 Z= 0.293 Chirality : 0.060 0.123 234 Planarity : 0.001 0.006 258 Dihedral : 8.575 43.549 224 Min Nonbonded Distance : 2.697 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.003 0.001 PHE F 19 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 1524) covalent geometry : angle 0.50440 ( 2046) hydrogen bonds : bond 0.06231 ( 4) hydrogen bonds : angle 9.22940 ( 12) *********************** 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 28 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.032 Fit side-chains REVERT: C 14 HIS cc_start: 0.8481 (m90) cc_final: 0.8220 (m90) REVERT: A 22 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8522 (tp30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0457 time to fit residues: 1.4334 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 : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.106796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084437 restraints weight = 2029.533| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.70 r_work: 0.3274 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 1524 Z= 0.275 Angle : 0.608 4.583 2046 Z= 0.344 Chirality : 0.065 0.146 234 Planarity : 0.002 0.006 258 Dihedral : 4.848 14.406 204 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 10 PHE 0.012 0.002 PHE B 20 HIS 0.004 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00665 ( 1524) covalent geometry : angle 0.60819 ( 2046) hydrogen bonds : bond 0.07139 ( 4) hydrogen bonds : angle 8.91989 ( 12) *********************** 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 : 0.033 Fit side-chains REVERT: D 22 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8461 (tp30) REVERT: F 23 ASP cc_start: 0.8429 (p0) cc_final: 0.8172 (p0) REVERT: B 23 ASP cc_start: 0.8448 (p0) cc_final: 0.8150 (p0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0544 time to fit residues: 1.4511 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 : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.113523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.090297 restraints weight = 1921.376| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.81 r_work: 0.3388 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2363 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= 0.101 Angle : 0.485 3.459 2046 Z= 0.275 Chirality : 0.059 0.126 234 Planarity : 0.001 0.004 258 Dihedral : 4.267 12.636 204 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 3.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 10 PHE 0.004 0.001 PHE A 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 1524) covalent geometry : angle 0.48536 ( 2046) hydrogen bonds : bond 0.06169 ( 4) hydrogen bonds : angle 8.77264 ( 12) *********************** 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 25 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.059 Fit side-chains REVERT: D 22 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8276 (tp30) REVERT: B 23 ASP cc_start: 0.8397 (p0) cc_final: 0.8131 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0995 time to fit residues: 2.7621 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 : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083866 restraints weight = 1991.751| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.75 r_work: 0.3264 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 1524 Z= 0.252 Angle : 0.603 4.610 2046 Z= 0.337 Chirality : 0.062 0.136 234 Planarity : 0.002 0.010 258 Dihedral : 4.831 14.666 204 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 10 PHE 0.013 0.002 PHE B 20 HIS 0.004 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 1524) covalent geometry : angle 0.60294 ( 2046) hydrogen bonds : bond 0.07104 ( 4) hydrogen bonds : angle 8.80100 ( 12) *********************** 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 : 0.056 Fit side-chains REVERT: D 22 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8460 (tp30) REVERT: A 23 ASP cc_start: 0.8311 (p0) cc_final: 0.8108 (p0) REVERT: B 23 ASP cc_start: 0.8532 (p0) cc_final: 0.8223 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0853 time to fit residues: 2.3698 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 : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.110164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086464 restraints weight = 1958.402| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.74 r_work: 0.3315 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1524 Z= 0.182 Angle : 0.557 4.574 2046 Z= 0.309 Chirality : 0.061 0.133 234 Planarity : 0.002 0.008 258 Dihedral : 4.599 13.607 204 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 10 PHE 0.010 0.002 PHE B 20 HIS 0.003 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 1524) covalent geometry : angle 0.55744 ( 2046) hydrogen bonds : bond 0.06477 ( 4) hydrogen bonds : angle 8.75280 ( 12) *********************** 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 : 0.055 Fit side-chains REVERT: D 22 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8409 (tp30) REVERT: B 23 ASP cc_start: 0.8480 (p0) cc_final: 0.8209 (p0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0842 time to fit residues: 2.3515 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 : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 overall best weight: 0.6056 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.118499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094275 restraints weight = 1847.616| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.79 r_work: 0.3458 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1524 Z= 0.080 Angle : 0.466 3.707 2046 Z= 0.263 Chirality : 0.059 0.123 234 Planarity : 0.001 0.007 258 Dihedral : 4.010 11.851 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.58), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR C 10 PHE 0.003 0.001 PHE B 20 HIS 0.002 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 1524) covalent geometry : angle 0.46564 ( 2046) hydrogen bonds : bond 0.05318 ( 4) hydrogen bonds : angle 8.50345 ( 12) *********************** 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 22 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.070 Fit side-chains REVERT: B 23 ASP cc_start: 0.8410 (p0) cc_final: 0.8208 (p0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0915 time to fit residues: 2.2353 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 : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.117677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093649 restraints weight = 1908.250| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.79 r_work: 0.3459 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2936 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= 0.088 Angle : 0.459 3.533 2046 Z= 0.260 Chirality : 0.058 0.121 234 Planarity : 0.001 0.009 258 Dihedral : 3.884 11.025 204 Min Nonbonded Distance : 2.659 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.05 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 10 PHE 0.004 0.001 PHE B 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 1524) covalent geometry : angle 0.45880 ( 2046) hydrogen bonds : bond 0.05635 ( 4) hydrogen bonds : angle 8.28962 ( 12) *********************** 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 : 0.059 Fit side-chains REVERT: B 23 ASP cc_start: 0.8406 (p0) cc_final: 0.8177 (p0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0885 time to fit residues: 2.1702 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 : 0.068 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.111030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.087195 restraints weight = 1941.304| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.73 r_work: 0.3322 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1524 Z= 0.209 Angle : 0.557 4.209 2046 Z= 0.312 Chirality : 0.061 0.130 234 Planarity : 0.002 0.010 258 Dihedral : 4.458 13.289 204 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.59), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.11 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 10 PHE 0.011 0.002 PHE B 20 HIS 0.004 0.002 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 1524) covalent geometry : angle 0.55699 ( 2046) hydrogen bonds : bond 0.06512 ( 4) hydrogen bonds : angle 8.57193 ( 12) *********************** 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 23 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.059 Fit side-chains REVERT: D 22 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8378 (tp30) REVERT: B 23 ASP cc_start: 0.8508 (p0) cc_final: 0.8260 (p0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0896 time to fit residues: 2.2918 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 : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.115114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091091 restraints weight = 1908.335| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.76 r_work: 0.3417 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2766 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= 0.103 Angle : 0.487 3.774 2046 Z= 0.273 Chirality : 0.058 0.123 234 Planarity : 0.001 0.011 258 Dihedral : 4.087 11.774 204 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.60), 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 TYR 0.008 0.001 TYR C 10 PHE 0.005 0.001 PHE E 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 1524) covalent geometry : angle 0.48724 ( 2046) hydrogen bonds : bond 0.05711 ( 4) hydrogen bonds : angle 8.39126 ( 12) ********************** 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 21 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.080 Fit side-chains REVERT: B 23 ASP cc_start: 0.8457 (p0) cc_final: 0.8186 (p0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0993 time to fit residues: 2.3240 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 : 0.058 ------------------------------------------------------------------------------- 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: 0.2980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.118836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094265 restraints weight = 1858.058| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.80 r_work: 0.3451 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1524 Z= 0.092 Angle : 0.467 3.975 2046 Z= 0.264 Chirality : 0.058 0.121 234 Planarity : 0.001 0.010 258 Dihedral : 3.857 11.243 204 Min Nonbonded Distance : 2.655 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.61), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.03 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 10 PHE 0.004 0.001 PHE B 20 HIS 0.002 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 1524) covalent geometry : angle 0.46735 ( 2046) hydrogen bonds : bond 0.05535 ( 4) hydrogen bonds : angle 8.23138 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 573.84 seconds wall clock time: 10 minutes 40.71 seconds (640.71 seconds total)