Starting phenix.real_space_refine on Wed Jul 23 16:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgy_50433/07_2025/9fgy_50433_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgy_50433/07_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_50433/07_2025/9fgy_50433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgy_50433/07_2025/9fgy_50433.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgy_50433/07_2025/9fgy_50433_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgy_50433/07_2025/9fgy_50433_trim.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.85, per 1000 atoms: 1.29 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: 0.92 Conformation dependent library (CDL) restraints added in 462.4 milliseconds 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: 0.31 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: 1.22 Time building geometry restraints manager: 1.12 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: 3.980 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.510 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (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 TRP 0.005 0.001 TRP D 62 HIS 0.001 0.000 HIS C 54 PHE 0.003 0.001 PHE D 34 TYR 0.008 0.001 TYR D 23 ARG 0.002 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.24102 ( 73) hydrogen bonds : angle 9.26765 ( 174) SS BOND : bond 0.00140 ( 5) SS BOND : angle 1.08141 ( 10) covalent geometry : bond 0.00205 ( 1983) covalent geometry : angle 0.42024 ( 2682) *********************** 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 : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2445 time to fit residues: 11.0589 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** D 121 GLN ** 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 = 0.4550 r_free = 0.4550 target = 0.245238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.231447 restraints weight = 6592.559| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 1.44 r_work: 0.4361 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4262 r_free = 0.4262 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1988 Z= 0.191 Angle : 0.588 3.694 2692 Z= 0.338 Chirality : 0.040 0.124 286 Planarity : 0.005 0.039 349 Dihedral : 5.078 44.509 284 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.53), residues: 250 helix: 0.71 (0.74), residues: 58 sheet: 0.53 (0.68), residues: 64 loop : 0.20 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 62 HIS 0.000 0.000 HIS D 15 PHE 0.009 0.001 PHE D 34 TYR 0.019 0.003 TYR C 33 ARG 0.004 0.001 ARG C 82 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 73) hydrogen bonds : angle 6.71156 ( 174) SS BOND : bond 0.00568 ( 5) SS BOND : angle 1.32221 ( 10) covalent geometry : bond 0.00423 ( 1983) covalent geometry : angle 0.58397 ( 2682) *********************** 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 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.285 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: 33 average time/residue: 0.2545 time to fit residues: 9.9891 Evaluate side-chains 30 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.242523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.228787 restraints weight = 6719.769| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 1.45 r_work: 0.4317 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1988 Z= 0.181 Angle : 0.553 3.907 2692 Z= 0.320 Chirality : 0.040 0.128 286 Planarity : 0.005 0.040 349 Dihedral : 5.880 56.610 284 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 10.89 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.51), residues: 250 helix: 0.53 (0.72), residues: 58 sheet: 0.26 (0.64), residues: 69 loop : -0.34 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 123 HIS 0.003 0.001 HIS D 15 PHE 0.007 0.001 PHE D 34 TYR 0.016 0.002 TYR C 114 ARG 0.006 0.001 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.05383 ( 73) hydrogen bonds : angle 6.44831 ( 174) SS BOND : bond 0.00506 ( 5) SS BOND : angle 1.31120 ( 10) covalent geometry : bond 0.00399 ( 1983) covalent geometry : angle 0.54871 ( 2682) *********************** 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 41 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.2751 time to fit residues: 12.1936 Evaluate side-chains 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.241535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.228784 restraints weight = 6716.243| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 1.36 r_work: 0.4319 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4236 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4239 r_free = 0.4239 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 = 0.4239 r_free = 0.4239 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1988 Z= 0.162 Angle : 0.539 4.342 2692 Z= 0.310 Chirality : 0.040 0.133 286 Planarity : 0.005 0.039 349 Dihedral : 5.941 57.805 284 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.48 % Allowed : 12.87 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.51), residues: 250 helix: 0.70 (0.75), residues: 57 sheet: 0.23 (0.64), residues: 69 loop : -0.64 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 62 HIS 0.003 0.001 HIS D 15 PHE 0.004 0.001 PHE D 3 TYR 0.013 0.002 TYR C 94 ARG 0.002 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 73) hydrogen bonds : angle 6.12485 ( 174) SS BOND : bond 0.00436 ( 5) SS BOND : angle 1.59222 ( 10) covalent geometry : bond 0.00359 ( 1983) covalent geometry : angle 0.53140 ( 2682) *********************** 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 : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6010 (mtp180) cc_final: 0.5806 (ttp-170) outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.2617 time to fit residues: 10.6683 Evaluate side-chains 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR 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 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 5 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.242859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.230820 restraints weight = 6770.374| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 1.35 r_work: 0.4330 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4253 r_free = 0.4253 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4253 r_free = 0.4253 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1988 Z= 0.113 Angle : 0.478 4.034 2692 Z= 0.275 Chirality : 0.037 0.124 286 Planarity : 0.004 0.038 349 Dihedral : 5.326 46.834 284 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.98 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.52), residues: 250 helix: 0.93 (0.78), residues: 57 sheet: 0.36 (0.64), residues: 69 loop : -0.45 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 123 HIS 0.001 0.001 HIS D 15 PHE 0.003 0.001 PHE C 68 TYR 0.010 0.002 TYR C 33 ARG 0.001 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 73) hydrogen bonds : angle 5.87739 ( 174) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.54489 ( 10) covalent geometry : bond 0.00249 ( 1983) covalent geometry : angle 0.46953 ( 2682) *********************** 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 36 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.4180 time to fit residues: 16.1706 Evaluate side-chains 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.0010 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.4511 r_free = 0.4511 target = 0.240550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.227586 restraints weight = 6862.223| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 1.39 r_work: 0.4323 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4235 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4234 r_free = 0.4234 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 = 0.4234 r_free = 0.4234 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1988 Z= 0.143 Angle : 0.513 5.945 2692 Z= 0.291 Chirality : 0.038 0.128 286 Planarity : 0.004 0.037 349 Dihedral : 5.339 42.279 284 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.52), residues: 250 helix: 0.95 (0.79), residues: 57 sheet: 0.36 (0.64), residues: 69 loop : -0.67 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 62 HIS 0.002 0.001 HIS D 15 PHE 0.002 0.001 PHE D 34 TYR 0.014 0.002 TYR C 114 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 73) hydrogen bonds : angle 5.89333 ( 174) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.35071 ( 10) covalent geometry : bond 0.00315 ( 1983) covalent geometry : angle 0.50697 ( 2682) *********************** 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 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.3140 time to fit residues: 13.5509 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 : 0.218 ------------------------------------------------------------------------------- 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 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 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 = 0.4497 r_free = 0.4497 target = 0.239135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.226859 restraints weight = 6800.305| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.34 r_work: 0.4296 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 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 = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1988 Z= 0.150 Angle : 0.526 5.997 2692 Z= 0.299 Chirality : 0.039 0.126 286 Planarity : 0.004 0.036 349 Dihedral : 5.317 34.771 284 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.97 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.51), residues: 250 helix: 0.88 (0.77), residues: 57 sheet: 0.15 (0.62), residues: 69 loop : -0.76 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 117 HIS 0.002 0.001 HIS D 15 PHE 0.002 0.001 PHE C 37 TYR 0.014 0.002 TYR C 94 ARG 0.003 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 73) hydrogen bonds : angle 5.96058 ( 174) SS BOND : bond 0.00424 ( 5) SS BOND : angle 1.29943 ( 10) covalent geometry : bond 0.00331 ( 1983) covalent geometry : angle 0.52062 ( 2682) *********************** 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 40 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 0.2966 time to fit residues: 12.9095 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 : 0.377 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.240773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.228706 restraints weight = 6949.450| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 1.36 r_work: 0.4332 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4247 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4248 r_free = 0.4248 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1988 Z= 0.115 Angle : 0.487 4.301 2692 Z= 0.276 Chirality : 0.038 0.126 286 Planarity : 0.004 0.035 349 Dihedral : 4.965 21.479 284 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.51), residues: 250 helix: 0.92 (0.78), residues: 57 sheet: 0.21 (0.62), residues: 69 loop : -0.65 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 117 HIS 0.001 0.000 HIS D 15 PHE 0.002 0.001 PHE C 68 TYR 0.011 0.002 TYR C 114 ARG 0.002 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 73) hydrogen bonds : angle 5.74810 ( 174) SS BOND : bond 0.00303 ( 5) SS BOND : angle 1.24849 ( 10) covalent geometry : bond 0.00248 ( 1983) covalent geometry : angle 0.48217 ( 2682) *********************** 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 39 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.3794 time to fit residues: 16.0011 Evaluate side-chains 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.239167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.227313 restraints weight = 6767.945| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 1.33 r_work: 0.4298 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4213 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4228 r_free = 0.4228 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1988 Z= 0.150 Angle : 0.522 5.028 2692 Z= 0.297 Chirality : 0.039 0.128 286 Planarity : 0.004 0.035 349 Dihedral : 5.281 28.980 284 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.52), residues: 250 helix: 0.91 (0.78), residues: 57 sheet: 0.15 (0.58), residues: 78 loop : -0.82 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 117 HIS 0.002 0.001 HIS D 15 PHE 0.003 0.001 PHE C 37 TYR 0.014 0.002 TYR C 94 ARG 0.002 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 73) hydrogen bonds : angle 5.86798 ( 174) SS BOND : bond 0.00404 ( 5) SS BOND : angle 1.19555 ( 10) covalent geometry : bond 0.00330 ( 1983) covalent geometry : angle 0.51774 ( 2682) *********************** 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 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.2688 time to fit residues: 11.1321 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 : 0.301 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.234582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.221838 restraints weight = 6950.657| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.40 r_work: 0.4239 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4198 r_free = 0.4198 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4198 r_free = 0.4198 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1988 Z= 0.154 Angle : 0.527 4.966 2692 Z= 0.300 Chirality : 0.039 0.129 286 Planarity : 0.004 0.035 349 Dihedral : 5.386 32.050 284 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.53), residues: 250 helix: 0.89 (0.78), residues: 57 sheet: 0.12 (0.59), residues: 78 loop : -0.84 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 117 HIS 0.002 0.001 HIS D 15 PHE 0.003 0.001 PHE C 37 TYR 0.014 0.002 TYR C 94 ARG 0.002 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 73) hydrogen bonds : angle 5.87842 ( 174) SS BOND : bond 0.00420 ( 5) SS BOND : angle 1.22600 ( 10) covalent geometry : bond 0.00341 ( 1983) covalent geometry : angle 0.52248 ( 2682) ********************** 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 38 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.2686 time to fit residues: 11.1222 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 : 0.296 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.1632 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.235127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.221942 restraints weight = 6863.011| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.54 r_work: 0.4339 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.4247 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4201 r_free = 0.4201 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4201 r_free = 0.4201 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.4379 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= 0.092 Angle : 0.471 4.908 2692 Z= 0.264 Chirality : 0.037 0.125 286 Planarity : 0.003 0.033 349 Dihedral : 4.880 28.080 284 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.98 % Allowed : 15.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.54), residues: 250 helix: 1.01 (0.79), residues: 57 sheet: 0.42 (0.61), residues: 76 loop : -0.47 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 117 HIS 0.000 0.000 HIS D 15 PHE 0.004 0.001 PHE C 37 TYR 0.008 0.001 TYR D 23 ARG 0.002 0.000 ARG D 112 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 73) hydrogen bonds : angle 5.54638 ( 174) SS BOND : bond 0.00189 ( 5) SS BOND : angle 1.32681 ( 10) covalent geometry : bond 0.00197 ( 1983) covalent geometry : angle 0.46528 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4317.17 seconds wall clock time: 76 minutes 15.96 seconds (4575.96 seconds total)