Starting phenix.real_space_refine on Fri Aug 22 14:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1j_36793/08_2025/8k1j_36793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1j_36793/08_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_36793/08_2025/8k1j_36793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1j_36793/08_2025/8k1j_36793.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1j_36793/08_2025/8k1j_36793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1j_36793/08_2025/8k1j_36793.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.44, per 1000 atoms: 0.35 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: 0.40 Conformation dependent library (CDL) restraints added in 114.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.64 Time building geometry restraints manager: 0.51 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 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: 0.570 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.050 Find NCS groups from input model: 0.040 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG A 47 TYR 0.014 0.001 TYR B 18 PHE 0.004 0.000 PHE A 135 TRP 0.002 0.000 TRP A 184 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00124 ( 4156) covalent geometry : angle 0.34094 ( 5644) hydrogen bonds : bond 0.09170 ( 333) hydrogen bonds : angle 4.06201 ( 981) *********************** 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 : 0.168 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: 0.7947 time to fit residues: 46.4569 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.191128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141111 restraints weight = 4156.479| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.03 r_work: 0.3556 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4156 Z= 0.169 Angle : 0.514 5.808 5644 Z= 0.283 Chirality : 0.038 0.125 650 Planarity : 0.003 0.016 664 Dihedral : 6.529 47.080 952 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 11.03 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.12 (0.37), residues: 476 helix: 3.97 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.21 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.029 0.002 TYR A 85 PHE 0.012 0.002 PHE B 223 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4156) covalent geometry : angle 0.51379 ( 5644) hydrogen bonds : bond 0.04734 ( 333) hydrogen bonds : angle 3.40741 ( 981) *********************** 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 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.7650 (tp40) cc_final: 0.7266 (mp10) REVERT: A 244 LEU cc_start: 0.7080 (tt) cc_final: 0.6690 (tp) REVERT: B 180 GLN cc_start: 0.7652 (tp40) cc_final: 0.7266 (mp10) REVERT: B 244 LEU cc_start: 0.7071 (tt) cc_final: 0.6676 (tp) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.8103 time to fit residues: 47.2436 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.187529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136900 restraints weight = 4114.339| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.01 r_work: 0.3512 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.147 Angle : 0.469 5.923 5644 Z= 0.256 Chirality : 0.036 0.138 650 Planarity : 0.003 0.019 664 Dihedral : 5.940 42.089 952 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.70 % Allowed : 11.03 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.03 (0.37), residues: 476 helix: 3.93 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.02 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.024 0.002 TYR B 85 PHE 0.010 0.001 PHE B 135 TRP 0.002 0.001 TRP A 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4156) covalent geometry : angle 0.46865 ( 5644) hydrogen bonds : bond 0.04743 ( 333) hydrogen bonds : angle 3.39309 ( 981) *********************** 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 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.145 Fit side-chains REVERT: A 140 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6931 (mm) REVERT: A 180 GLN cc_start: 0.7772 (tp40) cc_final: 0.7391 (mp10) REVERT: A 190 TYR cc_start: 0.8838 (t80) cc_final: 0.8494 (t80) REVERT: B 140 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6920 (mm) REVERT: B 180 GLN cc_start: 0.7749 (tp40) cc_final: 0.7360 (mp10) REVERT: B 190 TYR cc_start: 0.8827 (t80) cc_final: 0.8471 (t80) outliers start: 11 outliers final: 3 residues processed: 52 average time/residue: 0.8953 time to fit residues: 47.6102 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET 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 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.181595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130423 restraints weight = 4091.676| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.00 r_work: 0.3198 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4156 Z= 0.166 Angle : 0.494 5.361 5644 Z= 0.272 Chirality : 0.037 0.131 650 Planarity : 0.003 0.020 664 Dihedral : 5.502 35.604 952 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.77 (0.38), residues: 476 helix: 3.79 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.27 (0.72), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 245 TYR 0.028 0.002 TYR B 85 PHE 0.009 0.001 PHE A 16 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4156) covalent geometry : angle 0.49373 ( 5644) hydrogen bonds : bond 0.05493 ( 333) hydrogen bonds : angle 3.47961 ( 981) *********************** 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 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.164 Fit side-chains REVERT: A 39 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7565 (pt0) REVERT: A 156 MET cc_start: 0.5995 (mmm) cc_final: 0.5776 (tpt) REVERT: A 180 GLN cc_start: 0.7919 (tp40) cc_final: 0.7534 (mp10) REVERT: A 190 TYR cc_start: 0.8976 (t80) cc_final: 0.8609 (t80) REVERT: B 39 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7573 (pt0) REVERT: B 140 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7107 (mm) REVERT: B 180 GLN cc_start: 0.7901 (tp40) cc_final: 0.7522 (mp10) REVERT: B 190 TYR cc_start: 0.8964 (t80) cc_final: 0.8588 (t80) outliers start: 9 outliers final: 3 residues processed: 66 average time/residue: 0.7895 time to fit residues: 53.3050 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 140 LEU 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 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 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 = 0.4110 r_free = 0.4110 target = 0.182095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131772 restraints weight = 4103.911| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.97 r_work: 0.3224 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.147 Angle : 0.476 6.955 5644 Z= 0.262 Chirality : 0.036 0.154 650 Planarity : 0.003 0.021 664 Dihedral : 5.248 33.794 952 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 11.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.69 (0.38), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.37 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 245 TYR 0.019 0.002 TYR B 85 PHE 0.008 0.001 PHE A 135 TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4156) covalent geometry : angle 0.47583 ( 5644) hydrogen bonds : bond 0.05203 ( 333) hydrogen bonds : angle 3.41140 ( 981) *********************** 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 74 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.157 Fit side-chains REVERT: A 39 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7553 (pt0) REVERT: A 47 ARG cc_start: 0.7028 (ttp80) cc_final: 0.6803 (ttt-90) REVERT: A 180 GLN cc_start: 0.7862 (tp40) cc_final: 0.7481 (mp10) REVERT: A 190 TYR cc_start: 0.8969 (t80) cc_final: 0.8571 (t80) REVERT: B 39 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7571 (pt0) REVERT: B 180 GLN cc_start: 0.7835 (tp40) cc_final: 0.7374 (mp10) REVERT: B 190 TYR cc_start: 0.8952 (t80) cc_final: 0.8544 (t80) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 0.8124 time to fit residues: 55.7354 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.182878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132243 restraints weight = 4204.445| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.01 r_work: 0.3464 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4156 Z= 0.133 Angle : 0.469 7.444 5644 Z= 0.256 Chirality : 0.036 0.162 650 Planarity : 0.003 0.021 664 Dihedral : 5.097 34.667 952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.23 % Allowed : 14.46 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.73 (0.38), residues: 476 helix: 3.77 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.35 (0.71), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 245 TYR 0.015 0.001 TYR B 85 PHE 0.008 0.001 PHE A 109 TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4156) covalent geometry : angle 0.46868 ( 5644) hydrogen bonds : bond 0.04953 ( 333) hydrogen bonds : angle 3.39250 ( 981) *********************** 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 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.125 Fit side-chains REVERT: A 39 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7531 (pt0) REVERT: A 47 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6742 (ttt-90) REVERT: A 140 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6968 (mm) REVERT: A 180 GLN cc_start: 0.7724 (tp40) cc_final: 0.7234 (mp10) REVERT: A 190 TYR cc_start: 0.8926 (t80) cc_final: 0.8501 (t80) REVERT: B 39 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7511 (pt0) REVERT: B 47 ARG cc_start: 0.6928 (ttt-90) cc_final: 0.6661 (ttt-90) REVERT: B 180 GLN cc_start: 0.7704 (tp40) cc_final: 0.7216 (mp10) REVERT: B 190 TYR cc_start: 0.8918 (t80) cc_final: 0.8552 (t80) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.7809 time to fit residues: 55.1123 Evaluate side-chains 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.181793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130930 restraints weight = 4222.682| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.01 r_work: 0.2953 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.145 Angle : 0.482 8.060 5644 Z= 0.265 Chirality : 0.036 0.172 650 Planarity : 0.003 0.021 664 Dihedral : 4.993 36.349 952 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.45 % Allowed : 13.48 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.64 (0.38), residues: 476 helix: 3.72 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.44 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.012 0.001 TYR B 85 PHE 0.009 0.001 PHE A 135 TRP 0.002 0.001 TRP B 184 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4156) covalent geometry : angle 0.48245 ( 5644) hydrogen bonds : bond 0.05122 ( 333) hydrogen bonds : angle 3.41009 ( 981) *********************** 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: 10 poor density : 62 time to evaluate : 0.154 Fit side-chains REVERT: A 39 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7099 (pt0) REVERT: A 140 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6348 (mm) REVERT: A 180 GLN cc_start: 0.7095 (tp40) cc_final: 0.6614 (mp10) REVERT: A 190 TYR cc_start: 0.8678 (t80) cc_final: 0.8299 (t80) REVERT: B 39 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7104 (pt0) REVERT: B 180 GLN cc_start: 0.7078 (tp40) cc_final: 0.6597 (mp10) REVERT: B 190 TYR cc_start: 0.8671 (t80) cc_final: 0.8282 (t80) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.7723 time to fit residues: 54.5019 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.181635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131211 restraints weight = 4105.479| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.97 r_work: 0.3290 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.044 4156 Z= 0.145 Angle : 0.490 8.426 5644 Z= 0.267 Chirality : 0.036 0.174 650 Planarity : 0.003 0.021 664 Dihedral : 4.930 37.471 952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.47 % Allowed : 14.71 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.65 (0.38), residues: 476 helix: 3.73 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.45 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.012 0.001 TYR B 85 PHE 0.008 0.001 PHE A 109 TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4156) covalent geometry : angle 0.48961 ( 5644) hydrogen bonds : bond 0.05107 ( 333) hydrogen bonds : angle 3.42522 ( 981) *********************** 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 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.151 Fit side-chains REVERT: A 39 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7479 (pt0) REVERT: A 140 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6900 (mm) REVERT: A 180 GLN cc_start: 0.7714 (tp40) cc_final: 0.7218 (mp10) REVERT: A 190 TYR cc_start: 0.8947 (t80) cc_final: 0.8583 (t80) REVERT: B 39 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7497 (pt0) REVERT: B 47 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6775 (ttt-90) REVERT: B 180 GLN cc_start: 0.7695 (tp40) cc_final: 0.7202 (mp10) REVERT: B 190 TYR cc_start: 0.8938 (t80) cc_final: 0.8566 (t80) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.8134 time to fit residues: 54.0240 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.183161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132695 restraints weight = 4147.389| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.98 r_work: 0.3475 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3778 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= 0.132 Angle : 0.478 8.899 5644 Z= 0.262 Chirality : 0.036 0.176 650 Planarity : 0.003 0.030 664 Dihedral : 4.844 38.048 952 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 14.95 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.72 (0.38), residues: 476 helix: 3.77 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.38 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.011 0.001 TYR B 85 PHE 0.009 0.001 PHE A 109 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4156) covalent geometry : angle 0.47818 ( 5644) hydrogen bonds : bond 0.04861 ( 333) hydrogen bonds : angle 3.38071 ( 981) *********************** 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: 5 poor density : 58 time to evaluate : 0.164 Fit side-chains REVERT: A 39 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7456 (pt0) REVERT: A 140 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6913 (mm) REVERT: A 180 GLN cc_start: 0.7687 (tp40) cc_final: 0.7185 (mp10) REVERT: A 190 TYR cc_start: 0.8927 (t80) cc_final: 0.8554 (t80) REVERT: B 39 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7509 (pt0) REVERT: B 135 PHE cc_start: 0.8023 (t80) cc_final: 0.7792 (t80) REVERT: B 156 MET cc_start: 0.5811 (tpp) cc_final: 0.5489 (tpt) REVERT: B 180 GLN cc_start: 0.7671 (tp40) cc_final: 0.7168 (mp10) REVERT: B 190 TYR cc_start: 0.8915 (t80) cc_final: 0.8510 (t80) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.9009 time to fit residues: 55.2752 Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.181226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130825 restraints weight = 4118.815| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.96 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.150 Angle : 0.501 8.714 5644 Z= 0.275 Chirality : 0.037 0.178 650 Planarity : 0.003 0.021 664 Dihedral : 4.877 39.603 952 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.23 % Allowed : 14.95 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.64 (0.38), residues: 476 helix: 3.72 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.43 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.012 0.001 TYR B 85 PHE 0.008 0.001 PHE A 109 TRP 0.002 0.001 TRP A 78 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4156) covalent geometry : angle 0.50072 ( 5644) hydrogen bonds : bond 0.05233 ( 333) hydrogen bonds : angle 3.44529 ( 981) ********************** 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 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.154 Fit side-chains REVERT: A 39 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7450 (pt0) REVERT: A 180 GLN cc_start: 0.7720 (tp40) cc_final: 0.7224 (mp10) REVERT: A 190 TYR cc_start: 0.8957 (t80) cc_final: 0.8573 (t80) REVERT: A 245 ARG cc_start: 0.6815 (ptp-170) cc_final: 0.6551 (ptp-170) REVERT: B 39 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7472 (pt0) REVERT: B 180 GLN cc_start: 0.7702 (tp40) cc_final: 0.7207 (mp10) REVERT: B 190 TYR cc_start: 0.8957 (t80) cc_final: 0.8596 (t80) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.8466 time to fit residues: 51.1218 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL 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 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.181733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131458 restraints weight = 4137.906| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.97 r_work: 0.3291 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.145 Angle : 0.498 8.745 5644 Z= 0.273 Chirality : 0.037 0.180 650 Planarity : 0.003 0.021 664 Dihedral : 4.870 40.165 952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.98 % Allowed : 15.44 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.65 (0.38), residues: 476 helix: 3.72 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.39 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.012 0.001 TYR B 85 PHE 0.008 0.001 PHE A 109 TRP 0.003 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4156) covalent geometry : angle 0.49848 ( 5644) hydrogen bonds : bond 0.05144 ( 333) hydrogen bonds : angle 3.44348 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1707.94 seconds wall clock time: 29 minutes 49.42 seconds (1789.42 seconds total)