Starting phenix.real_space_refine on Wed Sep 17 03:00:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.map" model { file = "/net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0f_61946/09_2025/9k0f_61946.cif" } resolution = 2.8 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= 0.002 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 9 5.16 5 C 1380 2.51 5 N 360 2.21 5 O 366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2115 Number of models: 1 Model: "" Number of chains: 17 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 256 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "G" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 110 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 256 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "L" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 110 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "N" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 256 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "J" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 110 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "O" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 0.80, per 1000 atoms: 0.38 Number of scatterers: 2115 At special positions: 0 Unit cell: (82.17, 89.64, 34.03, 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 9 16.00 O 366 8.00 N 360 7.00 C 1380 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: 0.16 Conformation dependent library (CDL) restraints added in 126.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.558A pdb=" N GLN E 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL D 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU E 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.611A pdb=" N ILE E 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.773A pdb=" N VAL E 40 " --> pdb=" O ILE D 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 19 removed outlier: 7.076A pdb=" N GLU G 22 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 31 through 33 removed outlier: 6.401A pdb=" N ILE G 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.668A pdb=" N VAL G 40 " --> pdb=" O ILE H 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 36 removed outlier: 8.893A pdb=" N ILE I 31 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N LEU L 34 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY I 33 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL L 36 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET I 35 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE M 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE I 32 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY M 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.808A pdb=" N VAL I 40 " --> pdb=" O ILE L 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 18 through 19 removed outlier: 6.430A pdb=" N VAL K 18 " --> pdb=" O PHE N 19 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 670 1.33 - 1.45: 262 1.45 - 1.56: 1189 1.56 - 1.68: 0 1.68 - 1.79: 18 Bond restraints: 2139 Sorted by residual: bond pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CG LEU M 34 " pdb=" CD1 LEU M 34 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CG LEU L 34 " pdb=" CD1 LEU L 34 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CB LYS D 16 " pdb=" CG LYS D 16 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CG LEU D 17 " pdb=" CD1 LEU D 17 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 ... (remaining 2134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 2552 1.01 - 2.02: 242 2.02 - 3.03: 46 3.03 - 4.04: 15 4.04 - 5.05: 10 Bond angle restraints: 2865 Sorted by residual: angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 111.37 115.46 -4.09 1.64e+00 3.72e-01 6.21e+00 angle pdb=" N GLU D 22 " pdb=" CA GLU D 22 " pdb=" C GLU D 22 " ideal model delta sigma weight residual 111.37 115.43 -4.06 1.64e+00 3.72e-01 6.13e+00 angle pdb=" C ALA G 21 " pdb=" N GLU G 22 " pdb=" CA GLU G 22 " ideal model delta sigma weight residual 121.94 117.75 4.19 1.76e+00 3.23e-01 5.66e+00 angle pdb=" C GLU E 22 " pdb=" N ASP E 23 " pdb=" CA ASP E 23 " ideal model delta sigma weight residual 122.76 118.94 3.82 1.63e+00 3.76e-01 5.48e+00 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 110.80 115.51 -4.71 2.13e+00 2.20e-01 4.89e+00 ... (remaining 2860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 1084 15.82 - 31.63: 76 31.63 - 47.45: 23 47.45 - 63.27: 4 63.27 - 79.08: 4 Dihedral angle restraints: 1191 sinusoidal: 429 harmonic: 762 Sorted by residual: dihedral pdb=" CA ALA F 21 " pdb=" C ALA F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ALA E 21 " pdb=" C ALA E 21 " pdb=" N GLU E 22 " pdb=" CA GLU E 22 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA D 21 " pdb=" C ALA D 21 " pdb=" N GLU D 22 " pdb=" CA GLU D 22 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 117 0.026 - 0.052: 109 0.052 - 0.078: 21 0.078 - 0.104: 62 0.104 - 0.130: 27 Chirality restraints: 336 Sorted by residual: chirality pdb=" CA GLU E 22 " pdb=" N GLU E 22 " pdb=" C GLU E 22 " pdb=" CB GLU E 22 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA GLU D 22 " pdb=" N GLU D 22 " pdb=" C GLU D 22 " pdb=" CB GLU D 22 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL D 24 " pdb=" N VAL D 24 " pdb=" C VAL D 24 " pdb=" CB VAL D 24 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 333 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 23 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C ASP E 23 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP E 23 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL E 24 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 23 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" C ASP F 23 " 0.017 2.00e-02 2.50e+03 pdb=" O ASP F 23 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL F 24 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 14 " 0.008 2.00e-02 2.50e+03 7.07e-03 7.49e-01 pdb=" CG HIS N 14 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS N 14 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 14 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS N 14 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS N 14 " 0.002 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 840 2.93 - 3.42: 1845 3.42 - 3.91: 3308 3.91 - 4.41: 3610 4.41 - 4.90: 7057 Nonbonded interactions: 16660 Sorted by model distance: nonbonded pdb=" N ASP E 23 " pdb=" OD1 ASP E 23 " model vdw 2.437 3.120 nonbonded pdb=" N ASP D 23 " pdb=" OD1 ASP D 23 " model vdw 2.452 3.120 nonbonded pdb=" OG SER F 8 " pdb=" N GLY F 9 " model vdw 2.509 3.120 nonbonded pdb=" OG SER D 8 " pdb=" N GLY D 9 " model vdw 2.517 3.120 nonbonded pdb=" N ASP F 23 " pdb=" OD1 ASP F 23 " model vdw 2.554 3.120 ... (remaining 16655 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' and resid 12 through 42) selection = (chain 'E' and resid 12 through 42) selection = (chain 'F' and resid 12 through 42) selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'O' } 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: 3.470 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.008 0.038 2139 Z= 0.352 Angle : 0.716 5.049 2865 Z= 0.390 Chirality : 0.058 0.130 336 Planarity : 0.002 0.013 354 Dihedral : 13.305 79.083 711 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -2.77 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR O 10 PHE 0.008 0.002 PHE J 19 HIS 0.006 0.002 HIS N 14 Details of bonding type rmsd covalent geometry : bond 0.00842 ( 2139) covalent geometry : angle 0.71584 ( 2865) hydrogen bonds : bond 0.12168 ( 24) hydrogen bonds : angle 6.48052 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.5275 time to fit residues: 25.3238 Evaluate side-chains 39 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS K 13 HIS ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN D 13 HIS N 13 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN J 15 GLN O 13 HIS ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106106 restraints weight = 2588.888| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.77 r_work: 0.3465 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2139 Z= 0.102 Angle : 0.519 5.301 2865 Z= 0.272 Chirality : 0.056 0.126 336 Planarity : 0.001 0.007 354 Dihedral : 4.881 19.873 282 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.94 % Allowed : 13.62 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.91 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR K 10 PHE 0.006 0.001 PHE K 20 HIS 0.002 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2139) covalent geometry : angle 0.51862 ( 2865) hydrogen bonds : bond 0.01536 ( 24) hydrogen bonds : angle 4.28711 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.090 Fit side-chains REVERT: N 13 HIS cc_start: 0.6942 (m90) cc_final: 0.6565 (m90) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.5590 time to fit residues: 23.9867 Evaluate side-chains 36 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.137472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103255 restraints weight = 2528.432| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.78 r_work: 0.3405 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2139 Z= 0.120 Angle : 0.516 4.858 2865 Z= 0.271 Chirality : 0.056 0.125 336 Planarity : 0.001 0.009 354 Dihedral : 4.785 21.014 282 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.88 % Allowed : 17.84 % Favored : 80.28 % 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: -1.57 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR K 10 PHE 0.006 0.001 PHE K 19 HIS 0.003 0.000 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2139) covalent geometry : angle 0.51592 ( 2865) hydrogen bonds : bond 0.01293 ( 24) hydrogen bonds : angle 4.05156 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.094 Fit side-chains REVERT: D 23 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7663 (p0) REVERT: N 13 HIS cc_start: 0.6969 (m90) cc_final: 0.6577 (m90) REVERT: F 23 ASP cc_start: 0.8147 (p0) cc_final: 0.7804 (p0) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 0.5849 time to fit residues: 23.8802 Evaluate side-chains 38 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain N residue 14 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100208 restraints weight = 2553.428| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.75 r_work: 0.3359 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2139 Z= 0.172 Angle : 0.556 5.423 2865 Z= 0.295 Chirality : 0.056 0.124 336 Planarity : 0.002 0.010 354 Dihedral : 5.000 22.069 282 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.82 % Allowed : 16.90 % Favored : 80.28 % 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: -1.35 (0.51), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR K 10 PHE 0.007 0.001 PHE K 19 HIS 0.004 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 2139) covalent geometry : angle 0.55642 ( 2865) hydrogen bonds : bond 0.01284 ( 24) hydrogen bonds : angle 4.08861 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.091 Fit side-chains REVERT: N 13 HIS cc_start: 0.7003 (m90) cc_final: 0.6614 (m90) REVERT: F 23 ASP cc_start: 0.8291 (p0) cc_final: 0.7958 (p0) REVERT: O 14 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7816 (p-80) REVERT: O 16 LYS cc_start: 0.8751 (mppt) cc_final: 0.8549 (mptt) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.5241 time to fit residues: 21.9439 Evaluate side-chains 40 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 14 HIS Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103841 restraints weight = 2528.565| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.76 r_work: 0.3424 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2139 Z= 0.109 Angle : 0.497 5.194 2865 Z= 0.263 Chirality : 0.055 0.124 336 Planarity : 0.001 0.009 354 Dihedral : 4.632 20.609 282 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.88 % Allowed : 19.25 % Favored : 78.87 % 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: -1.17 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.005 0.001 PHE O 19 HIS 0.003 0.000 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2139) covalent geometry : angle 0.49748 ( 2865) hydrogen bonds : bond 0.01179 ( 24) hydrogen bonds : angle 3.89128 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.081 Fit side-chains REVERT: E 23 ASP cc_start: 0.7893 (p0) cc_final: 0.7683 (p0) REVERT: N 13 HIS cc_start: 0.6980 (m90) cc_final: 0.6609 (m90) REVERT: F 23 ASP cc_start: 0.8108 (p0) cc_final: 0.7804 (p0) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.5402 time to fit residues: 23.1493 Evaluate side-chains 39 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098773 restraints weight = 2504.210| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.73 r_work: 0.3328 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2139 Z= 0.227 Angle : 0.612 6.091 2865 Z= 0.323 Chirality : 0.057 0.125 336 Planarity : 0.002 0.011 354 Dihedral : 5.184 23.521 282 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.23 % Allowed : 16.43 % Favored : 79.34 % 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: -1.14 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR K 10 PHE 0.008 0.002 PHE K 19 HIS 0.005 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 2139) covalent geometry : angle 0.61175 ( 2865) hydrogen bonds : bond 0.01301 ( 24) hydrogen bonds : angle 4.25151 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.083 Fit side-chains REVERT: H 22 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: N 13 HIS cc_start: 0.6951 (m90) cc_final: 0.6555 (m90) REVERT: F 23 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8102 (p0) REVERT: O 14 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7784 (p-80) outliers start: 9 outliers final: 1 residues processed: 45 average time/residue: 0.5084 time to fit residues: 23.3651 Evaluate side-chains 44 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100350 restraints weight = 2540.420| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.73 r_work: 0.3369 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2139 Z= 0.169 Angle : 0.589 7.140 2865 Z= 0.307 Chirality : 0.056 0.125 336 Planarity : 0.002 0.010 354 Dihedral : 4.990 22.822 282 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.82 % Allowed : 18.78 % Favored : 78.40 % 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: -1.02 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR K 10 PHE 0.006 0.001 PHE O 19 HIS 0.005 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2139) covalent geometry : angle 0.58907 ( 2865) hydrogen bonds : bond 0.01256 ( 24) hydrogen bonds : angle 4.14720 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.094 Fit side-chains REVERT: H 22 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: N 13 HIS cc_start: 0.7009 (m90) cc_final: 0.6609 (m90) REVERT: O 14 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7901 (p-80) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.5117 time to fit residues: 21.4572 Evaluate side-chains 40 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 overall best weight: 1.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101360 restraints weight = 2521.360| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.72 r_work: 0.3374 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2139 Z= 0.161 Angle : 0.584 7.652 2865 Z= 0.306 Chirality : 0.056 0.124 336 Planarity : 0.001 0.010 354 Dihedral : 4.990 22.615 282 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 20.19 % Favored : 77.46 % 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: -0.98 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 10 PHE 0.006 0.001 PHE O 19 HIS 0.005 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2139) covalent geometry : angle 0.58371 ( 2865) hydrogen bonds : bond 0.01207 ( 24) hydrogen bonds : angle 4.15511 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.079 Fit side-chains REVERT: H 22 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: N 13 HIS cc_start: 0.6964 (m90) cc_final: 0.6630 (m90) REVERT: O 14 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7885 (p-80) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.4602 time to fit residues: 19.2382 Evaluate side-chains 41 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099668 restraints weight = 2545.652| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.75 r_work: 0.3359 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2139 Z= 0.201 Angle : 0.620 7.167 2865 Z= 0.324 Chirality : 0.057 0.125 336 Planarity : 0.002 0.011 354 Dihedral : 5.154 23.490 282 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.82 % Allowed : 18.78 % Favored : 78.40 % 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: -0.96 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 10 PHE 0.007 0.002 PHE K 19 HIS 0.005 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 2139) covalent geometry : angle 0.61961 ( 2865) hydrogen bonds : bond 0.01274 ( 24) hydrogen bonds : angle 4.24085 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.055 Fit side-chains REVERT: H 22 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: N 13 HIS cc_start: 0.6984 (m90) cc_final: 0.6633 (m90) REVERT: O 14 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7823 (p-80) outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.5290 time to fit residues: 22.7005 Evaluate side-chains 42 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101561 restraints weight = 2536.178| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.75 r_work: 0.3378 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2139 Z= 0.153 Angle : 0.583 7.429 2865 Z= 0.304 Chirality : 0.056 0.124 336 Planarity : 0.001 0.010 354 Dihedral : 4.920 22.317 282 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.41 % Allowed : 21.60 % 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 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: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.005 0.001 PHE K 19 HIS 0.004 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2139) covalent geometry : angle 0.58252 ( 2865) hydrogen bonds : bond 0.01214 ( 24) hydrogen bonds : angle 4.13249 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.072 Fit side-chains REVERT: H 22 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: N 13 HIS cc_start: 0.6978 (m90) cc_final: 0.6640 (m90) REVERT: O 14 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7628 (p-80) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.5162 time to fit residues: 21.0783 Evaluate side-chains 40 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain O residue 14 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0070 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN N 15 GLN ** O 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.139102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105710 restraints weight = 2570.470| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.69 r_work: 0.3459 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2139 Z= 0.096 Angle : 0.527 7.129 2865 Z= 0.275 Chirality : 0.055 0.124 336 Planarity : 0.001 0.009 354 Dihedral : 4.578 20.389 282 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.88 % Allowed : 20.66 % Favored : 77.46 % 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: -0.80 (0.52), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR D 10 PHE 0.005 0.001 PHE G 19 HIS 0.003 0.000 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 2139) covalent geometry : angle 0.52710 ( 2865) hydrogen bonds : bond 0.01126 ( 24) hydrogen bonds : angle 3.91749 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.15 seconds wall clock time: 20 minutes 28.94 seconds (1228.94 seconds total)