Starting phenix.real_space_refine on Wed Jul 23 18:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh3_50438/07_2025/9fh3_50438.cif" } resolution = 3.9 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= 0.300 sd= 1.508 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1280 2.51 5 N 360 2.21 5 O 340 1.98 5 H 2110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4100 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "F" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Time building chain proxies: 2.60, per 1000 atoms: 0.63 Number of scatterers: 4100 At special positions: 0 Unit cell: (72.624, 66.096, 44.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 340 8.00 N 360 7.00 C 1280 6.00 H 2110 1.00 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: 1.08 Conformation dependent library (CDL) restraints added in 271.5 milliseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 46.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 4 removed outlier: 6.427A pdb=" N TYR C 1 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 4 " --> pdb=" O TYR C 1 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 3 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.686A pdb=" N LEU C 8 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.833A pdb=" N LEU C 19 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 20 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 21 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 16 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU E 19 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLY C 18 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N VAL E 21 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N MET C 20 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE E 16 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU G 19 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY E 18 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N VAL G 21 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N MET E 20 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE I 16 " --> pdb=" O ALA G 15 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE G 17 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY I 18 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.625A pdb=" N VAL C 25 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 7 through 9 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 21 removed outlier: 6.523A pdb=" N ILE B 16 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU D 19 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY B 18 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N VAL D 21 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N MET B 20 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE D 16 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU F 19 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY D 18 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N VAL F 21 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N MET D 20 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE F 16 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU H 19 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY F 18 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL H 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N MET F 20 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 16 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU J 19 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY H 18 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N VAL J 21 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N MET H 20 " --> pdb=" O VAL J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 26 55 hydrogen bonds defined for protein. 165 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: 1.18 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2110 1.13 - 1.30: 320 1.30 - 1.47: 650 1.47 - 1.64: 1020 1.64 - 1.81: 20 Bond restraints: 4120 Sorted by residual: bond pdb=" N LYS B 7 " pdb=" H LYS B 7 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 TYR G 1 " pdb=" HE1 TYR G 1 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER E 11 " pdb=" H SER E 11 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL A 9 " pdb=" H VAL A 9 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 TYR I 1 " pdb=" HD1 TYR I 1 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 4964 1.67 - 3.34: 1618 3.34 - 5.02: 570 5.02 - 6.69: 288 6.69 - 8.36: 40 Bond angle restraints: 7480 Sorted by residual: angle pdb=" N HIS F 4 " pdb=" CA HIS F 4 " pdb=" C HIS F 4 " ideal model delta sigma weight residual 109.07 116.86 -7.79 1.52e+00 4.33e-01 2.63e+01 angle pdb=" N HIS E 4 " pdb=" CA HIS E 4 " pdb=" C HIS E 4 " ideal model delta sigma weight residual 109.07 116.84 -7.77 1.52e+00 4.33e-01 2.61e+01 angle pdb=" N HIS D 4 " pdb=" CA HIS D 4 " pdb=" C HIS D 4 " ideal model delta sigma weight residual 109.07 116.73 -7.66 1.52e+00 4.33e-01 2.54e+01 angle pdb=" N HIS G 4 " pdb=" CA HIS G 4 " pdb=" C HIS G 4 " ideal model delta sigma weight residual 109.07 116.59 -7.52 1.52e+00 4.33e-01 2.45e+01 angle pdb=" N HIS C 4 " pdb=" CA HIS C 4 " pdb=" C HIS C 4 " ideal model delta sigma weight residual 109.07 116.59 -7.52 1.52e+00 4.33e-01 2.45e+01 ... (remaining 7475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.05: 1578 13.05 - 26.10: 114 26.10 - 39.15: 37 39.15 - 52.20: 46 52.20 - 65.25: 85 Dihedral angle restraints: 1860 sinusoidal: 1040 harmonic: 820 Sorted by residual: dihedral pdb=" CA GLU J 2 " pdb=" C GLU J 2 " pdb=" N VAL J 3 " pdb=" CA VAL J 3 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU I 2 " pdb=" C GLU I 2 " pdb=" N VAL I 3 " pdb=" CA VAL I 3 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU G 2 " pdb=" C GLU G 2 " pdb=" N VAL G 3 " pdb=" CA VAL G 3 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 1857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 133 0.062 - 0.124: 102 0.124 - 0.187: 51 0.187 - 0.249: 15 0.249 - 0.311: 19 Chirality restraints: 320 Sorted by residual: chirality pdb=" CA HIS F 4 " pdb=" N HIS F 4 " pdb=" C HIS F 4 " pdb=" CB HIS F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA HIS D 4 " pdb=" N HIS D 4 " pdb=" C HIS D 4 " pdb=" CB HIS D 4 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA HIS G 4 " pdb=" N HIS G 4 " pdb=" C HIS G 4 " pdb=" CB HIS G 4 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 317 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 4 " 0.026 2.00e-02 2.50e+03 4.83e-02 5.26e+01 pdb=" CG HIS B 4 " -0.079 2.00e-02 2.50e+03 pdb=" ND1 HIS B 4 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 HIS B 4 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS B 4 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS B 4 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS B 4 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS B 4 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS B 4 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 4 " -0.025 2.00e-02 2.50e+03 4.69e-02 4.96e+01 pdb=" CG HIS A 4 " 0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS A 4 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 HIS A 4 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 4 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS A 4 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS A 4 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 HIS A 4 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 HIS A 4 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 4 " -0.028 2.00e-02 2.50e+03 4.60e-02 4.76e+01 pdb=" CG HIS C 4 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS C 4 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS C 4 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS C 4 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS C 4 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 HIS C 4 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 HIS C 4 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS C 4 " -0.027 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 750 2.35 - 2.91: 8713 2.91 - 3.47: 10675 3.47 - 4.04: 13547 4.04 - 4.60: 20008 Nonbonded interactions: 53693 Sorted by model distance: nonbonded pdb="HE22 GLN D 6 " pdb="HG13 ILE F 26 " model vdw 1.784 2.270 nonbonded pdb="HE22 GLN C 6 " pdb="HG13 ILE E 26 " model vdw 1.788 2.270 nonbonded pdb="HE22 GLN E 6 " pdb="HG13 ILE G 26 " model vdw 1.789 2.270 nonbonded pdb=" O ILE E 26 " pdb=" H ALA G 27 " model vdw 1.796 2.450 nonbonded pdb=" O ILE F 26 " pdb=" H ALA H 27 " model vdw 1.797 2.450 ... (remaining 53688 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.011 0.034 2010 Z= 0.728 Angle : 2.106 7.791 2690 Z= 1.369 Chirality : 0.117 0.311 320 Planarity : 0.009 0.033 330 Dihedral : 11.275 36.158 690 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 0.16 (0.45), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.13 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS G 5 TYR 0.041 0.012 TYR A 1 Details of bonding type rmsd hydrogen bonds : bond 0.11610 ( 55) hydrogen bonds : angle 7.80585 ( 165) covalent geometry : bond 0.01128 ( 2010) covalent geometry : angle 2.10558 ( 2690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: G 17 ILE cc_start: 0.8836 (mp) cc_final: 0.8602 (mp) REVERT: H 17 ILE cc_start: 0.8924 (mp) cc_final: 0.8622 (mp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1478 time to fit residues: 13.6389 Evaluate side-chains 52 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.272522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5541 r_free = 0.5541 target = 0.218817 restraints weight = 12881.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5583 r_free = 0.5583 target = 0.222267 restraints weight = 5348.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5619 r_free = 0.5619 target = 0.224142 restraints weight = 2594.793| |-----------------------------------------------------------------------------| r_work (final): 0.5146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2010 Z= 0.256 Angle : 0.762 5.355 2690 Z= 0.442 Chirality : 0.061 0.153 320 Planarity : 0.003 0.009 330 Dihedral : 6.268 14.220 280 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.50 % Allowed : 17.00 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 4 TYR 0.008 0.002 TYR J 1 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 55) hydrogen bonds : angle 5.89754 ( 165) covalent geometry : bond 0.00498 ( 2010) covalent geometry : angle 0.76178 ( 2690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6846 (m-80) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1437 time to fit residues: 8.4360 Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 TYR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 1 TYR Chi-restraints excluded: chain E residue 1 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.274706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5533 r_free = 0.5533 target = 0.220285 restraints weight = 13069.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5579 r_free = 0.5579 target = 0.223771 restraints weight = 5486.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5606 r_free = 0.5606 target = 0.225642 restraints weight = 2684.772| |-----------------------------------------------------------------------------| r_work (final): 0.5141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2010 Z= 0.206 Angle : 0.645 5.118 2690 Z= 0.380 Chirality : 0.061 0.141 320 Planarity : 0.002 0.006 330 Dihedral : 5.371 12.748 280 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.50 % Allowed : 19.00 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 4 TYR 0.008 0.002 TYR I 1 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 55) hydrogen bonds : angle 5.60020 ( 165) covalent geometry : bond 0.00406 ( 2010) covalent geometry : angle 0.64517 ( 2690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: F 1 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: H 1 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6055 (m-80) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 0.1634 time to fit residues: 9.0635 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 TYR Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain H residue 1 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.264011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5559 r_free = 0.5559 target = 0.221908 restraints weight = 13188.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.5615 r_free = 0.5615 target = 0.225616 restraints weight = 5345.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5641 r_free = 0.5641 target = 0.227612 restraints weight = 2549.253| |-----------------------------------------------------------------------------| r_work (final): 0.5169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2010 Z= 0.175 Angle : 0.568 4.615 2690 Z= 0.333 Chirality : 0.060 0.138 320 Planarity : 0.002 0.005 330 Dihedral : 4.824 11.023 280 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.00 % Allowed : 19.00 % Favored : 78.00 % 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: -0.58 (0.39), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 4 TYR 0.006 0.001 TYR J 1 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 55) hydrogen bonds : angle 5.39124 ( 165) covalent geometry : bond 0.00337 ( 2010) covalent geometry : angle 0.56831 ( 2690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: G 1 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: I 1 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6184 (m-80) outliers start: 6 outliers final: 0 residues processed: 44 average time/residue: 0.1542 time to fit residues: 8.9251 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Chi-restraints excluded: chain I residue 1 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.269249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5613 r_free = 0.5613 target = 0.229560 restraints weight = 13444.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5645 r_free = 0.5645 target = 0.232738 restraints weight = 5781.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.234503 restraints weight = 2825.201| |-----------------------------------------------------------------------------| r_work (final): 0.5213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2010 Z= 0.101 Angle : 0.492 3.884 2690 Z= 0.288 Chirality : 0.060 0.131 320 Planarity : 0.001 0.004 330 Dihedral : 4.228 9.874 280 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.00 % Allowed : 22.50 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.42), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.27 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 4 TYR 0.003 0.001 TYR I 1 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 55) hydrogen bonds : angle 5.13971 ( 165) covalent geometry : bond 0.00202 ( 2010) covalent geometry : angle 0.49154 ( 2690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: G 1 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6515 (m-80) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1458 time to fit residues: 8.4766 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.281235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5592 r_free = 0.5592 target = 0.227392 restraints weight = 13376.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5630 r_free = 0.5630 target = 0.230841 restraints weight = 5705.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5678 r_free = 0.5678 target = 0.232765 restraints weight = 2759.573| |-----------------------------------------------------------------------------| r_work (final): 0.5201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2010 Z= 0.119 Angle : 0.493 4.023 2690 Z= 0.288 Chirality : 0.060 0.135 320 Planarity : 0.001 0.005 330 Dihedral : 3.991 9.338 280 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.00 % Allowed : 22.00 % Favored : 76.00 % 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: -0.01 (0.44), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.00 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 4 TYR 0.005 0.001 TYR J 1 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 55) hydrogen bonds : angle 5.12387 ( 165) covalent geometry : bond 0.00236 ( 2010) covalent geometry : angle 0.49300 ( 2690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: G 1 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6559 (m-80) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.1548 time to fit residues: 8.6303 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Chi-restraints excluded: chain I residue 5 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.269156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5608 r_free = 0.5608 target = 0.228498 restraints weight = 13218.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5647 r_free = 0.5647 target = 0.232300 restraints weight = 5258.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5682 r_free = 0.5682 target = 0.234270 restraints weight = 2498.943| |-----------------------------------------------------------------------------| r_work (final): 0.5221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2010 Z= 0.093 Angle : 0.462 3.744 2690 Z= 0.271 Chirality : 0.060 0.142 320 Planarity : 0.001 0.005 330 Dihedral : 3.828 10.051 280 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.50 % Allowed : 22.50 % Favored : 77.00 % 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: 0.19 (0.45), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.16 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 4 TYR 0.003 0.001 TYR F 1 Details of bonding type rmsd hydrogen bonds : bond 0.02637 ( 55) hydrogen bonds : angle 5.03762 ( 165) covalent geometry : bond 0.00189 ( 2010) covalent geometry : angle 0.46191 ( 2690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 1 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6542 (m-80) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1782 time to fit residues: 10.4065 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.275003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5562 r_free = 0.5562 target = 0.221625 restraints weight = 13294.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.224913 restraints weight = 5601.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5631 r_free = 0.5631 target = 0.226718 restraints weight = 2741.766| |-----------------------------------------------------------------------------| r_work (final): 0.5170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2010 Z= 0.174 Angle : 0.524 4.467 2690 Z= 0.307 Chirality : 0.060 0.141 320 Planarity : 0.002 0.005 330 Dihedral : 4.088 10.724 280 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 20.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 4 TYR 0.008 0.002 TYR J 1 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 55) hydrogen bonds : angle 5.27814 ( 165) covalent geometry : bond 0.00328 ( 2010) covalent geometry : angle 0.52424 ( 2690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: G 1 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: H 1 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6142 (m-80) outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.1643 time to fit residues: 8.6587 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain I residue 5 HIS Chi-restraints excluded: chain J residue 1 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.267901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5604 r_free = 0.5604 target = 0.225424 restraints weight = 13163.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5648 r_free = 0.5648 target = 0.228978 restraints weight = 5328.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.230918 restraints weight = 2546.753| |-----------------------------------------------------------------------------| r_work (final): 0.5182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2010 Z= 0.112 Angle : 0.467 3.892 2690 Z= 0.273 Chirality : 0.060 0.134 320 Planarity : 0.001 0.005 330 Dihedral : 3.958 10.399 280 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.50 % Allowed : 21.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 4 TYR 0.005 0.001 TYR A 1 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 55) hydrogen bonds : angle 5.02156 ( 165) covalent geometry : bond 0.00227 ( 2010) covalent geometry : angle 0.46657 ( 2690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: G 1 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6596 (m-80) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.1452 time to fit residues: 7.7404 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Chi-restraints excluded: chain I residue 5 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.268002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5604 r_free = 0.5604 target = 0.226140 restraints weight = 13083.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5643 r_free = 0.5643 target = 0.229708 restraints weight = 5271.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5676 r_free = 0.5676 target = 0.231658 restraints weight = 2521.963| |-----------------------------------------------------------------------------| r_work (final): 0.5189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2010 Z= 0.100 Angle : 0.461 3.750 2690 Z= 0.269 Chirality : 0.060 0.132 320 Planarity : 0.001 0.006 330 Dihedral : 3.793 10.485 280 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.50 % Allowed : 21.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.17 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 4 TYR 0.006 0.001 TYR A 1 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 55) hydrogen bonds : angle 4.97321 ( 165) covalent geometry : bond 0.00207 ( 2010) covalent geometry : angle 0.46092 ( 2690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: G 1 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6643 (m-80) outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.1982 time to fit residues: 10.5906 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 TYR Chi-restraints excluded: chain G residue 1 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.264752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5567 r_free = 0.5567 target = 0.221827 restraints weight = 13131.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5615 r_free = 0.5615 target = 0.225458 restraints weight = 5415.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5640 r_free = 0.5640 target = 0.227363 restraints weight = 2593.441| |-----------------------------------------------------------------------------| r_work (final): 0.5173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2010 Z= 0.156 Angle : 0.510 4.202 2690 Z= 0.297 Chirality : 0.060 0.138 320 Planarity : 0.002 0.005 330 Dihedral : 3.924 12.369 280 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.00 % Allowed : 21.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.07 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 4 TYR 0.006 0.001 TYR I 1 Details of bonding type rmsd hydrogen bonds : bond 0.02736 ( 55) hydrogen bonds : angle 5.06127 ( 165) covalent geometry : bond 0.00302 ( 2010) covalent geometry : angle 0.51029 ( 2690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2326.76 seconds wall clock time: 40 minutes 46.15 seconds (2446.15 seconds total)