Starting phenix.real_space_refine on Fri Aug 22 14:03:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgy_50433/08_2025/9fgy_50433_trim.cif" } resolution = 3.16 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= 0.015 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 17 5.16 5 C 1197 2.51 5 N 356 2.21 5 O 377 1.98 5 H 1822 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3769 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Conformer: "B" Number of residues, atoms: 126, 1855 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} bond proxies already assigned to first conformer: 1871 Chain: "D" Number of atoms: 1907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 128, 1906 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1925 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AGOL C 201 " occ=0.20 ... (4 atoms not shown) pdb=" O3 AGOL C 201 " occ=0.20 Time building chain proxies: 1.84, per 1000 atoms: 0.49 Number of scatterers: 3769 At special positions: 0 Unit cell: (47.45, 63.51, 81.76, 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 17 16.00 O 377 8.00 N 356 7.00 C 1197 6.00 H 1822 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 94 " distance=2.03 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: 0.38 Conformation dependent library (CDL) restraints added in 217.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 458 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 29.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.560A pdb=" N SER C 30 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.829A pdb=" N TRP D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 removed outlier: 3.821A pdb=" N LEU D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.548A pdb=" N ASN D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 119 through 125 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.701A pdb=" N GLY C 10 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR C 33 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.535A pdb=" N TYR D 53 " --> pdb=" O ILE D 58 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 174 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: 0.99 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1822 1.03 - 1.23: 23 1.23 - 1.43: 852 1.43 - 1.62: 1085 1.62 - 1.82: 23 Bond restraints: 3805 Sorted by residual: bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N ASP C 1 " pdb=" H ASP C 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 AGOL C 201 " pdb=" C2 AGOL C 201 " ideal model delta sigma weight residual 1.514 1.542 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C2 AGOL C 201 " pdb=" O2 AGOL C 201 " ideal model delta sigma weight residual 1.410 1.385 0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C2 AGOL C 201 " pdb=" C3 AGOL C 201 " ideal model delta sigma weight residual 1.520 1.544 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 3800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 6476 1.08 - 2.16: 285 2.16 - 3.25: 12 3.25 - 4.33: 3 4.33 - 5.41: 2 Bond angle restraints: 6778 Sorted by residual: angle pdb=" C1 AGOL C 201 " pdb=" C2 AGOL C 201 " pdb=" C3 AGOL C 201 " ideal model delta sigma weight residual 110.15 104.74 5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" C ASN D 93 " pdb=" N CYS D 94 " pdb=" CA CYS D 94 " ideal model delta sigma weight residual 120.72 117.72 3.00 1.67e+00 3.59e-01 3.24e+00 angle pdb=" CA CYS D 76 " pdb=" CB CYS D 76 " pdb=" SG CYS D 76 " ideal model delta sigma weight residual 114.40 118.49 -4.09 2.30e+00 1.89e-01 3.16e+00 angle pdb=" CA GLN D 121 " pdb=" CB GLN D 121 " pdb=" CG GLN D 121 " ideal model delta sigma weight residual 114.10 117.50 -3.40 2.00e+00 2.50e-01 2.89e+00 angle pdb=" N VAL C 64 " pdb=" CA VAL C 64 " pdb=" C VAL C 64 " ideal model delta sigma weight residual 111.91 110.45 1.46 8.90e-01 1.26e+00 2.70e+00 ... (remaining 6773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1659 16.87 - 33.74: 111 33.74 - 50.60: 39 50.60 - 67.47: 10 67.47 - 84.34: 2 Dihedral angle restraints: 1821 sinusoidal: 972 harmonic: 849 Sorted by residual: dihedral pdb=" CG ARG D 125 " pdb=" CD ARG D 125 " pdb=" NE ARG D 125 " pdb=" CZ ARG D 125 " ideal model delta sinusoidal sigma weight residual 90.00 129.15 -39.15 2 1.50e+01 4.44e-03 8.50e+00 dihedral pdb=" CB ARG D 5 " pdb=" CG ARG D 5 " pdb=" CD ARG D 5 " pdb=" NE ARG D 5 " ideal model delta sinusoidal sigma weight residual 180.00 133.42 46.58 3 1.50e+01 4.44e-03 8.36e+00 dihedral pdb=" CG LYS D 97 " pdb=" CD LYS D 97 " pdb=" CE LYS D 97 " pdb=" NZ LYS D 97 " ideal model delta sinusoidal sigma weight residual 180.00 133.69 46.31 3 1.50e+01 4.44e-03 8.32e+00 ... (remaining 1818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 168 0.025 - 0.050: 84 0.050 - 0.075: 18 0.075 - 0.099: 9 0.099 - 0.124: 7 Chirality restraints: 286 Sorted by residual: chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL C 123 " pdb=" N VAL C 123 " pdb=" C VAL C 123 " pdb=" CB VAL C 123 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.07e-01 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 283 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 103 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO C 104 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 69 " -0.014 5.00e-02 4.00e+02 2.06e-02 6.79e-01 pdb=" N PRO D 70 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO D 70 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 70 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 94 " -0.004 2.00e-02 2.50e+03 8.07e-03 6.51e-01 pdb=" C CYS D 94 " 0.014 2.00e-02 2.50e+03 pdb=" O CYS D 94 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA D 95 " -0.005 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 212 2.19 - 2.79: 7615 2.79 - 3.39: 10541 3.39 - 4.00: 13636 4.00 - 4.60: 21116 Nonbonded interactions: 53120 Sorted by model distance: nonbonded pdb=" O TRP D 63 " pdb=" H CYS D 76 " model vdw 1.587 2.450 nonbonded pdb=" O ASN D 106 " pdb=" HE ARG D 112 " model vdw 1.672 2.450 nonbonded pdb=" O ALA C 108 " pdb=" HH TYR C 114 " model vdw 1.734 2.450 nonbonded pdb=" H THR D 51 " pdb=" OG SER D 60 " model vdw 1.759 2.450 nonbonded pdb=" OE1 GLU C 89 " pdb=" H AGLU C 89 " model vdw 1.786 2.450 ... (remaining 53115 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 6.490 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 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 : 0.002 0.032 1988 Z= 0.105 Angle : 0.425 5.411 2692 Z= 0.238 Chirality : 0.035 0.124 286 Planarity : 0.002 0.031 349 Dihedral : 13.070 84.337 702 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.32 (0.55), residues: 250 helix: 1.31 (0.78), residues: 56 sheet: 0.38 (0.63), residues: 63 loop : 1.17 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 125 TYR 0.008 0.001 TYR D 23 PHE 0.003 0.001 PHE D 34 TRP 0.005 0.001 TRP D 62 HIS 0.001 0.000 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 1983) covalent geometry : angle 0.42024 ( 2682) SS BOND : bond 0.00140 ( 5) SS BOND : angle 1.08141 ( 10) hydrogen bonds : bond 0.24102 ( 73) hydrogen bonds : angle 9.26765 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1205 time to fit residues: 5.3916 Evaluate side-chains 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.246841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.233070 restraints weight = 6664.209| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 1.44 r_work: 0.4380 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.4293 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4280 r_free = 0.4280 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1988 Z= 0.166 Angle : 0.561 3.627 2692 Z= 0.322 Chirality : 0.039 0.121 286 Planarity : 0.005 0.037 349 Dihedral : 4.747 38.980 284 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % 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: 0.72 (0.54), residues: 250 helix: 0.78 (0.74), residues: 58 sheet: 0.61 (0.68), residues: 64 loop : 0.42 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 82 TYR 0.018 0.002 TYR C 33 PHE 0.008 0.001 PHE D 34 TRP 0.010 0.002 TRP D 62 HIS 0.000 0.000 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 1983) covalent geometry : angle 0.55614 ( 2682) SS BOND : bond 0.00496 ( 5) SS BOND : angle 1.28577 ( 10) hydrogen bonds : bond 0.05128 ( 73) hydrogen bonds : angle 6.58742 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 35 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1207 time to fit residues: 4.8549 Evaluate side-chains 32 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.245937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.232812 restraints weight = 6660.355| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 1.39 r_work: 0.4359 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4278 r_free = 0.4278 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4278 r_free = 0.4278 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1988 Z= 0.132 Angle : 0.488 3.588 2692 Z= 0.281 Chirality : 0.038 0.126 286 Planarity : 0.004 0.039 349 Dihedral : 4.694 32.182 284 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.99 % Allowed : 10.89 % Favored : 88.12 % 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: 0.51 (0.53), residues: 250 helix: 0.88 (0.77), residues: 58 sheet: 0.52 (0.67), residues: 64 loop : 0.11 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.012 0.002 TYR C 33 PHE 0.007 0.001 PHE D 34 TRP 0.007 0.001 TRP D 108 HIS 0.001 0.000 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 1983) covalent geometry : angle 0.48320 ( 2682) SS BOND : bond 0.00389 ( 5) SS BOND : angle 1.25929 ( 10) hydrogen bonds : bond 0.04677 ( 73) hydrogen bonds : angle 6.15345 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.1822 time to fit residues: 7.7898 Evaluate side-chains 37 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.242900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.229797 restraints weight = 6731.814| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.39 r_work: 0.4317 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1988 Z= 0.158 Angle : 0.517 3.940 2692 Z= 0.298 Chirality : 0.039 0.128 286 Planarity : 0.005 0.040 349 Dihedral : 5.077 36.426 284 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.48 % Allowed : 11.39 % Favored : 86.14 % 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: 0.02 (0.51), residues: 250 helix: 0.71 (0.75), residues: 58 sheet: 0.27 (0.63), residues: 69 loop : -0.39 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 14 TYR 0.015 0.002 TYR C 33 PHE 0.007 0.001 PHE D 34 TRP 0.007 0.001 TRP D 62 HIS 0.002 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 1983) covalent geometry : angle 0.51250 ( 2682) SS BOND : bond 0.00442 ( 5) SS BOND : angle 1.21561 ( 10) hydrogen bonds : bond 0.04563 ( 73) hydrogen bonds : angle 6.01583 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 TRP cc_start: 0.7550 (m-90) cc_final: 0.7293 (m-90) outliers start: 5 outliers final: 5 residues processed: 35 average time/residue: 0.1273 time to fit residues: 5.2868 Evaluate side-chains 36 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.243570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.229962 restraints weight = 6881.396| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.49 r_work: 0.4329 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4236 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1988 Z= 0.119 Angle : 0.489 4.279 2692 Z= 0.279 Chirality : 0.038 0.127 286 Planarity : 0.004 0.038 349 Dihedral : 4.755 24.784 284 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.98 % Allowed : 12.87 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.52), residues: 250 helix: 0.86 (0.77), residues: 57 sheet: 0.39 (0.63), residues: 69 loop : -0.48 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 14 TYR 0.010 0.002 TYR C 33 PHE 0.002 0.001 PHE C 37 TRP 0.004 0.001 TRP D 123 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1983) covalent geometry : angle 0.47937 ( 2682) SS BOND : bond 0.00345 ( 5) SS BOND : angle 1.66721 ( 10) hydrogen bonds : bond 0.04221 ( 73) hydrogen bonds : angle 5.85956 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1527 time to fit residues: 6.3408 Evaluate side-chains 34 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.240617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.228172 restraints weight = 6693.525| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.30 r_work: 0.4312 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1988 Z= 0.165 Angle : 0.531 4.052 2692 Z= 0.305 Chirality : 0.039 0.129 286 Planarity : 0.005 0.039 349 Dihedral : 5.098 21.224 284 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.47 % Allowed : 13.37 % Favored : 83.17 % 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: -0.22 (0.51), residues: 250 helix: 0.70 (0.76), residues: 57 sheet: 0.33 (0.63), residues: 69 loop : -0.79 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 14 TYR 0.016 0.002 TYR C 114 PHE 0.003 0.001 PHE C 68 TRP 0.008 0.001 TRP D 62 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 1983) covalent geometry : angle 0.52318 ( 2682) SS BOND : bond 0.00460 ( 5) SS BOND : angle 1.56935 ( 10) hydrogen bonds : bond 0.04535 ( 73) hydrogen bonds : angle 5.97006 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1261 time to fit residues: 5.2192 Evaluate side-chains 37 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.241628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.229274 restraints weight = 6948.257| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.38 r_work: 0.4324 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4235 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1988 Z= 0.139 Angle : 0.496 4.167 2692 Z= 0.285 Chirality : 0.038 0.129 286 Planarity : 0.004 0.038 349 Dihedral : 5.073 30.246 284 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.97 % Allowed : 13.37 % Favored : 83.66 % 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: -0.18 (0.51), residues: 250 helix: 0.87 (0.77), residues: 57 sheet: 0.36 (0.62), residues: 69 loop : -0.84 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 14 TYR 0.011 0.002 TYR C 114 PHE 0.002 0.001 PHE C 37 TRP 0.017 0.001 TRP C 117 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 1983) covalent geometry : angle 0.48989 ( 2682) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.34973 ( 10) hydrogen bonds : bond 0.04275 ( 73) hydrogen bonds : angle 5.84006 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.1155 time to fit residues: 5.0789 Evaluate side-chains 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.238044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.225632 restraints weight = 6806.760| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 1.36 r_work: 0.4299 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4209 r_free = 0.4209 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1988 Z= 0.171 Angle : 0.540 4.238 2692 Z= 0.311 Chirality : 0.040 0.135 286 Planarity : 0.005 0.037 349 Dihedral : 5.463 35.127 284 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.97 % Allowed : 13.86 % Favored : 83.17 % 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: -0.32 (0.51), residues: 250 helix: 0.76 (0.76), residues: 57 sheet: 0.46 (0.65), residues: 69 loop : -1.06 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 14 TYR 0.017 0.002 TYR C 114 PHE 0.003 0.001 PHE C 37 TRP 0.011 0.001 TRP C 117 HIS 0.001 0.000 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 1983) covalent geometry : angle 0.53556 ( 2682) SS BOND : bond 0.00480 ( 5) SS BOND : angle 1.28342 ( 10) hydrogen bonds : bond 0.04659 ( 73) hydrogen bonds : angle 5.97650 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 PHE cc_start: 0.7493 (m-10) cc_final: 0.6838 (m-10) outliers start: 6 outliers final: 6 residues processed: 34 average time/residue: 0.1297 time to fit residues: 5.1661 Evaluate side-chains 36 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.231652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.218851 restraints weight = 6823.691| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 1.43 r_work: 0.4246 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1988 Z= 0.134 Angle : 0.497 4.233 2692 Z= 0.284 Chirality : 0.038 0.128 286 Planarity : 0.004 0.034 349 Dihedral : 5.258 35.623 284 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.47 % Allowed : 13.86 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.52), residues: 250 helix: 0.78 (0.77), residues: 57 sheet: 0.62 (0.65), residues: 67 loop : -0.89 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 14 TYR 0.012 0.002 TYR D 23 PHE 0.002 0.001 PHE C 37 TRP 0.011 0.001 TRP C 117 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 1983) covalent geometry : angle 0.49132 ( 2682) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.30563 ( 10) hydrogen bonds : bond 0.04215 ( 73) hydrogen bonds : angle 5.80931 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 36 average time/residue: 0.1272 time to fit residues: 5.3741 Evaluate side-chains 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 4 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 18 optimal weight: 0.0670 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.234286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.221400 restraints weight = 6878.105| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.46 r_work: 0.4295 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1988 Z= 0.093 Angle : 0.462 3.915 2692 Z= 0.262 Chirality : 0.037 0.125 286 Planarity : 0.003 0.032 349 Dihedral : 4.798 29.489 284 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.49 % Allowed : 16.34 % Favored : 82.18 % 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: 0.20 (0.54), residues: 250 helix: 0.91 (0.78), residues: 57 sheet: 0.69 (0.61), residues: 76 loop : -0.59 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 21 TYR 0.014 0.002 TYR D 23 PHE 0.003 0.001 PHE D 34 TRP 0.010 0.001 TRP C 117 HIS 0.001 0.000 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 1983) covalent geometry : angle 0.45586 ( 2682) SS BOND : bond 0.00204 ( 5) SS BOND : angle 1.31946 ( 10) hydrogen bonds : bond 0.03695 ( 73) hydrogen bonds : angle 5.57424 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 500 Ramachandran restraints generated. 250 Oldfield, 0 Emsley, 250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 124 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 PHE cc_start: 0.7443 (m-10) cc_final: 0.6809 (m-10) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.1147 time to fit residues: 4.5521 Evaluate side-chains 36 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.230855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.217836 restraints weight = 6826.189| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.44 r_work: 0.4232 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4148 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1988 Z= 0.144 Angle : 0.495 4.089 2692 Z= 0.285 Chirality : 0.039 0.127 286 Planarity : 0.004 0.034 349 Dihedral : 5.103 31.357 284 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.49 % Allowed : 15.84 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.53), residues: 250 helix: 0.84 (0.77), residues: 57 sheet: 0.72 (0.65), residues: 67 loop : -0.66 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 14 TYR 0.014 0.002 TYR D 23 PHE 0.002 0.001 PHE C 68 TRP 0.009 0.001 TRP C 117 HIS 0.001 0.001 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 1983) covalent geometry : angle 0.49108 ( 2682) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.17976 ( 10) hydrogen bonds : bond 0.04199 ( 73) hydrogen bonds : angle 5.69754 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.44 seconds wall clock time: 36 minutes 35.64 seconds (2195.64 seconds total)