Starting phenix.real_space_refine on Sun Apr 27 01:10:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1j_36793/04_2025/8k1j_36793.cif" } resolution = 3.0 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= 0.100 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 K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4069 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 110 Unusual residues: {' K': 5, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.24, per 1000 atoms: 0.80 Number of scatterers: 4069 At special positions: 0 Unit cell: (69.3, 71.5, 90.2, 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) K 5 19.00 S 32 16.00 O 710 8.00 N 616 7.00 C 2706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 479.6 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.638A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.764A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.634A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.901A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 333 hydrogen bonds defined for protein. 981 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: 0.97 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 664 1.33 - 1.45: 1092 1.45 - 1.57: 2352 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.94e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.64e-01 bond pdb=" C ILE B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.43e-01 bond pdb=" C GLU A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.42e-01 bond pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.33e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 5548 1.00 - 2.00: 75 2.00 - 3.00: 9 3.00 - 4.00: 6 4.00 - 5.00: 6 Bond angle restraints: 5644 Sorted by residual: angle pdb=" C THR A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.98 -3.80 2.37e+00 1.78e-01 2.57e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.93 -3.75 2.37e+00 1.78e-01 2.51e+00 angle pdb=" CA TYR A 18 " pdb=" CB TYR A 18 " pdb=" CG TYR A 18 " ideal model delta sigma weight residual 113.90 116.71 -2.81 1.80e+00 3.09e-01 2.44e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2433 16.20 - 32.39: 211 32.39 - 48.59: 36 48.59 - 64.79: 20 64.79 - 80.99: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG B 3 " pdb=" CD ARG B 3 " pdb=" NE ARG B 3 " pdb=" CZ ARG B 3 " ideal model delta sinusoidal sigma weight residual 180.00 -139.84 -40.16 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CG ARG A 3 " pdb=" CD ARG A 3 " pdb=" NE ARG A 3 " pdb=" CZ ARG A 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.85 -40.15 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 80.30 -80.30 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 437 0.021 - 0.043: 96 0.043 - 0.064: 82 0.064 - 0.086: 20 0.086 - 0.107: 15 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.86e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.85e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 18 " -0.009 2.00e-02 2.50e+03 6.07e-03 7.38e-01 pdb=" CG TYR B 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 18 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 18 " -0.009 2.00e-02 2.50e+03 5.99e-03 7.17e-01 pdb=" CG TYR A 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 18 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.006 2.00e-02 2.50e+03 4.21e-03 3.54e-01 pdb=" CG TYR A 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.002 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 1426 2.86 - 3.43: 4548 3.43 - 4.00: 7182 4.00 - 4.57: 10541 4.57 - 5.14: 14505 Nonbonded interactions: 38202 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.301 3.040 nonbonded pdb=" O TYR A 113 " pdb=" OH TYR B 18 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O TYR B 113 " model vdw 2.324 3.040 ... (remaining 38197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 248 or resid 301 through 303)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.001 0.012 4156 Z= 0.075 Angle : 0.341 4.999 5644 Z= 0.179 Chirality : 0.031 0.107 650 Planarity : 0.002 0.015 664 Dihedral : 13.842 80.987 1816 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 5.90 (0.38), residues: 476 helix: 4.48 (0.22), residues: 384 sheet: None (None), residues: 0 loop : 0.94 (0.85), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 184 HIS 0.002 0.000 HIS A 72 PHE 0.004 0.000 PHE A 135 TYR 0.014 0.001 TYR B 18 ARG 0.001 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.09170 ( 333) hydrogen bonds : angle 4.06201 ( 981) covalent geometry : bond 0.00124 ( 4156) covalent geometry : angle 0.34094 ( 5644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.7254 (tt) cc_final: 0.6627 (tp) REVERT: B 244 LEU cc_start: 0.7241 (tt) cc_final: 0.6615 (tp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.6301 time to fit residues: 95.4426 Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146904 restraints weight = 4042.678| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.87 r_work: 0.3622 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4156 Z= 0.151 Angle : 0.486 6.261 5644 Z= 0.266 Chirality : 0.037 0.122 650 Planarity : 0.003 0.014 664 Dihedral : 6.564 46.794 952 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 10.78 % Favored : 87.99 % 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: 5.29 (0.37), residues: 476 helix: 4.09 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.28 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.012 0.002 PHE B 223 TYR 0.024 0.002 TYR A 85 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 333) hydrogen bonds : angle 3.36163 ( 981) covalent geometry : bond 0.00332 ( 4156) covalent geometry : angle 0.48560 ( 5644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 180 GLN cc_start: 0.7664 (tp40) cc_final: 0.7291 (mp10) REVERT: A 244 LEU cc_start: 0.7065 (tt) cc_final: 0.6661 (tp) REVERT: B 180 GLN cc_start: 0.7655 (tp40) cc_final: 0.7278 (mp10) REVERT: B 244 LEU cc_start: 0.7062 (tt) cc_final: 0.6653 (tp) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 1.7336 time to fit residues: 94.3521 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 245 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.190143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139986 restraints weight = 4126.445| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.01 r_work: 0.3549 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.128 Angle : 0.443 5.694 5644 Z= 0.243 Chirality : 0.036 0.142 650 Planarity : 0.003 0.024 664 Dihedral : 5.836 40.483 952 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 10.78 % Favored : 87.01 % 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: 5.15 (0.37), residues: 476 helix: 4.01 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.10 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.011 0.001 PHE A 135 TYR 0.023 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 333) hydrogen bonds : angle 3.28715 ( 981) covalent geometry : bond 0.00276 ( 4156) covalent geometry : angle 0.44326 ( 5644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.428 Fit side-chains REVERT: A 140 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6858 (mm) REVERT: A 180 GLN cc_start: 0.7761 (tp40) cc_final: 0.7366 (mp10) REVERT: A 190 TYR cc_start: 0.8825 (t80) cc_final: 0.8456 (t80) REVERT: A 244 LEU cc_start: 0.7135 (tt) cc_final: 0.6772 (tp) REVERT: B 140 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6902 (mm) REVERT: B 180 GLN cc_start: 0.7762 (tp40) cc_final: 0.7365 (mp10) REVERT: B 190 TYR cc_start: 0.8811 (t80) cc_final: 0.8428 (t80) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 1.7544 time to fit residues: 98.9483 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.0000 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137388 restraints weight = 4125.641| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.00 r_work: 0.3516 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4156 Z= 0.128 Angle : 0.440 5.033 5644 Z= 0.241 Chirality : 0.036 0.140 650 Planarity : 0.003 0.023 664 Dihedral : 5.367 34.403 952 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 11.52 % Favored : 86.52 % 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: 5.09 (0.37), residues: 476 helix: 3.98 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.02 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 PHE 0.007 0.001 PHE A 109 TYR 0.021 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 333) hydrogen bonds : angle 3.30399 ( 981) covalent geometry : bond 0.00270 ( 4156) covalent geometry : angle 0.43976 ( 5644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.386 Fit side-chains REVERT: A 39 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7246 (pt0) REVERT: A 130 GLU cc_start: 0.7740 (tp30) cc_final: 0.7528 (tp30) REVERT: A 140 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 180 GLN cc_start: 0.7757 (tp40) cc_final: 0.7363 (mp10) REVERT: A 190 TYR cc_start: 0.8849 (t80) cc_final: 0.8453 (t80) REVERT: B 39 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7244 (pt0) REVERT: B 180 GLN cc_start: 0.7728 (tp40) cc_final: 0.7337 (mp10) REVERT: B 190 TYR cc_start: 0.8837 (t80) cc_final: 0.8432 (t80) outliers start: 8 outliers final: 2 residues processed: 63 average time/residue: 1.8213 time to fit residues: 117.3871 Evaluate side-chains 64 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.183689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132534 restraints weight = 4271.409| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.04 r_work: 0.3231 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.144 Angle : 0.476 6.978 5644 Z= 0.262 Chirality : 0.037 0.164 650 Planarity : 0.003 0.025 664 Dihedral : 5.079 33.572 952 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.72 % Allowed : 13.24 % Favored : 85.05 % 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: 4.89 (0.38), residues: 476 helix: 3.87 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.20 (0.72), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 PHE 0.010 0.001 PHE B 135 TYR 0.023 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 333) hydrogen bonds : angle 3.37892 ( 981) covalent geometry : bond 0.00319 ( 4156) covalent geometry : angle 0.47608 ( 5644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.416 Fit side-chains REVERT: A 39 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7518 (pt0) REVERT: A 140 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7030 (mm) REVERT: A 180 GLN cc_start: 0.7891 (tp40) cc_final: 0.7519 (mp10) REVERT: A 190 TYR cc_start: 0.8967 (t80) cc_final: 0.8572 (t80) REVERT: B 39 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7522 (pt0) REVERT: B 180 GLN cc_start: 0.7884 (tp40) cc_final: 0.7510 (mp10) REVERT: B 190 TYR cc_start: 0.8948 (t80) cc_final: 0.8541 (t80) REVERT: B 245 ARG cc_start: 0.7627 (ptp90) cc_final: 0.7385 (ptp-170) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 1.7392 time to fit residues: 117.5714 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.180766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130761 restraints weight = 4169.276| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.99 r_work: 0.2921 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4156 Z= 0.171 Angle : 0.513 7.232 5644 Z= 0.282 Chirality : 0.038 0.159 650 Planarity : 0.003 0.029 664 Dihedral : 5.099 36.376 952 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 13.48 % Favored : 84.56 % 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: 4.57 (0.38), residues: 476 helix: 3.67 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.47 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 PHE 0.009 0.001 PHE B 16 TYR 0.022 0.002 TYR B 85 ARG 0.005 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 333) hydrogen bonds : angle 3.52095 ( 981) covalent geometry : bond 0.00398 ( 4156) covalent geometry : angle 0.51320 ( 5644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.391 Fit side-chains REVERT: A 39 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7177 (pt0) REVERT: A 47 ARG cc_start: 0.6690 (ttp80) cc_final: 0.6451 (ttt-90) REVERT: A 140 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6501 (mm) REVERT: A 180 GLN cc_start: 0.7322 (tp40) cc_final: 0.6853 (mp10) REVERT: A 190 TYR cc_start: 0.8792 (t80) cc_final: 0.8410 (t80) REVERT: B 39 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7128 (pt0) REVERT: B 47 ARG cc_start: 0.6703 (ttp80) cc_final: 0.6501 (ttt-90) REVERT: B 180 GLN cc_start: 0.7287 (tp40) cc_final: 0.6812 (mp10) REVERT: B 190 TYR cc_start: 0.8791 (t80) cc_final: 0.8399 (t80) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 1.7386 time to fit residues: 117.4214 Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.181350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130855 restraints weight = 4156.600| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.98 r_work: 0.3448 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4156 Z= 0.148 Angle : 0.487 8.155 5644 Z= 0.267 Chirality : 0.037 0.171 650 Planarity : 0.003 0.026 664 Dihedral : 4.960 37.100 952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.72 % Allowed : 13.48 % Favored : 84.80 % 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: 4.56 (0.38), residues: 476 helix: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.51 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 78 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE B 109 TYR 0.018 0.001 TYR A 85 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 333) hydrogen bonds : angle 3.43605 ( 981) covalent geometry : bond 0.00325 ( 4156) covalent geometry : angle 0.48654 ( 5644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.375 Fit side-chains REVERT: A 39 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7516 (pt0) REVERT: A 44 GLU cc_start: 0.7657 (tp30) cc_final: 0.7444 (tp30) REVERT: A 47 ARG cc_start: 0.6967 (ttp80) cc_final: 0.6719 (ttt-90) REVERT: A 140 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6936 (mm) REVERT: A 180 GLN cc_start: 0.7719 (tp40) cc_final: 0.7219 (mp10) REVERT: B 39 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7508 (pt0) REVERT: B 180 GLN cc_start: 0.7707 (tp40) cc_final: 0.7209 (mp10) REVERT: B 190 TYR cc_start: 0.8937 (t80) cc_final: 0.8527 (t80) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 1.8762 time to fit residues: 132.5077 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.182341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132520 restraints weight = 4135.916| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.98 r_work: 0.3217 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4156 Z= 0.152 Angle : 0.497 8.390 5644 Z= 0.274 Chirality : 0.037 0.174 650 Planarity : 0.003 0.023 664 Dihedral : 4.936 38.281 952 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.47 % Allowed : 15.44 % Favored : 83.09 % 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: 4.60 (0.38), residues: 476 helix: 3.70 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.49 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.002 0.000 HIS B 98 PHE 0.008 0.001 PHE B 109 TYR 0.015 0.001 TYR B 85 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05315 ( 333) hydrogen bonds : angle 3.45741 ( 981) covalent geometry : bond 0.00338 ( 4156) covalent geometry : angle 0.49716 ( 5644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.394 Fit side-chains REVERT: A 39 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7593 (pt0) REVERT: A 140 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7107 (mm) REVERT: A 180 GLN cc_start: 0.7843 (tp40) cc_final: 0.7357 (mp10) REVERT: A 190 TYR cc_start: 0.9003 (t80) cc_final: 0.8634 (t80) REVERT: B 39 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7548 (pt0) REVERT: B 180 GLN cc_start: 0.7827 (tp40) cc_final: 0.7340 (mp10) REVERT: B 190 TYR cc_start: 0.8990 (t80) cc_final: 0.8612 (t80) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 1.8183 time to fit residues: 119.1396 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132086 restraints weight = 4163.958| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.98 r_work: 0.3464 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4156 Z= 0.138 Angle : 0.481 8.654 5644 Z= 0.265 Chirality : 0.036 0.175 650 Planarity : 0.003 0.022 664 Dihedral : 4.842 39.078 952 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 15.69 % Favored : 82.84 % 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: 4.71 (0.38), residues: 476 helix: 3.78 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.47 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE B 109 TYR 0.015 0.001 TYR B 85 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 333) hydrogen bonds : angle 3.41011 ( 981) covalent geometry : bond 0.00293 ( 4156) covalent geometry : angle 0.48116 ( 5644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.437 Fit side-chains REVERT: A 39 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7366 (pt0) REVERT: A 140 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6924 (mm) REVERT: A 156 MET cc_start: 0.5831 (tpp) cc_final: 0.5624 (tpt) REVERT: A 180 GLN cc_start: 0.7574 (tp40) cc_final: 0.7058 (mp10) REVERT: B 39 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7354 (pt0) REVERT: B 135 PHE cc_start: 0.7873 (t80) cc_final: 0.7600 (t80) REVERT: B 180 GLN cc_start: 0.7556 (tp40) cc_final: 0.7041 (mp10) REVERT: B 190 TYR cc_start: 0.8883 (t80) cc_final: 0.8482 (t80) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 2.6641 time to fit residues: 163.6416 Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.181616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131135 restraints weight = 4190.625| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.99 r_work: 0.2957 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4156 Z= 0.148 Angle : 0.501 9.095 5644 Z= 0.276 Chirality : 0.037 0.181 650 Planarity : 0.003 0.029 664 Dihedral : 4.856 40.212 952 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.23 % Allowed : 15.93 % Favored : 82.84 % 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: 4.69 (0.37), residues: 476 helix: 3.76 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.44 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE B 109 TYR 0.013 0.001 TYR B 85 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 333) hydrogen bonds : angle 3.43909 ( 981) covalent geometry : bond 0.00328 ( 4156) covalent geometry : angle 0.50141 ( 5644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.375 Fit side-chains REVERT: A 39 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7084 (pt0) REVERT: A 140 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6362 (mm) REVERT: A 180 GLN cc_start: 0.7079 (tp40) cc_final: 0.6597 (mp10) REVERT: B 39 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7046 (pt0) REVERT: B 180 GLN cc_start: 0.7062 (tp40) cc_final: 0.6580 (mp10) REVERT: B 190 TYR cc_start: 0.8674 (t80) cc_final: 0.8254 (t80) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 1.8583 time to fit residues: 108.3362 Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.183728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133507 restraints weight = 4089.095| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4156 Z= 0.130 Angle : 0.489 8.812 5644 Z= 0.268 Chirality : 0.036 0.176 650 Planarity : 0.003 0.030 664 Dihedral : 4.796 40.451 952 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 15.69 % Favored : 82.84 % 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: 4.77 (0.38), residues: 476 helix: 3.81 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.36 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE B 109 TYR 0.013 0.001 TYR B 85 ARG 0.007 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 333) hydrogen bonds : angle 3.40671 ( 981) covalent geometry : bond 0.00265 ( 4156) covalent geometry : angle 0.48897 ( 5644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3595.39 seconds wall clock time: 62 minutes 47.65 seconds (3767.65 seconds total)