Starting phenix.real_space_refine on Fri Aug 22 14:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1q_36799/08_2025/8k1q_36799.map" } resolution = 3.68 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= 0.001 sd= 0.078 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 2 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 702 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: 4058 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Unusual residues: {' K': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.44, per 1000 atoms: 0.35 Number of scatterers: 4058 At special positions: 0 Unit cell: (64.9, 73.7, 89.1, 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 2 19.00 S 32 16.00 O 702 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: 0.50 Conformation dependent library (CDL) restraints added in 189.7 milliseconds Enol-peptide restraints added in 953.7 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: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.604A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.952A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 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: 3.516A pdb=" N ILE B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.951A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 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 247 331 hydrogen bonds defined for protein. 969 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: 0.64 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: 677 1.33 - 1.45: 1082 1.45 - 1.57: 2349 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" CA LYS B 42 " pdb=" C LYS B 42 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 1.524 1.449 0.076 1.29e-02 6.01e+03 3.44e+01 bond pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.17e-02 7.31e+03 2.33e+01 bond pdb=" N MET B 156 " pdb=" CA MET B 156 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.17e-02 7.31e+03 2.26e+01 bond pdb=" CA ARG A 73 " pdb=" C ARG A 73 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.37e-02 5.33e+03 1.11e+01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5557 1.51 - 3.03: 55 3.03 - 4.54: 18 4.54 - 6.05: 10 6.05 - 7.56: 4 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N LYS A 42 " pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 111.40 103.84 7.56 1.22e+00 6.72e-01 3.84e+01 angle pdb=" N LYS B 42 " pdb=" CA LYS B 42 " pdb=" C LYS B 42 " ideal model delta sigma weight residual 111.40 103.84 7.56 1.22e+00 6.72e-01 3.84e+01 angle pdb=" C SER B 155 " pdb=" N MET B 156 " pdb=" CA MET B 156 " ideal model delta sigma weight residual 120.65 114.81 5.84 1.32e+00 5.74e-01 1.96e+01 angle pdb=" C SER A 155 " pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 120.65 114.88 5.77 1.32e+00 5.74e-01 1.91e+01 angle pdb=" C LYS A 42 " pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta sigma weight residual 121.54 114.17 7.37 1.91e+00 2.74e-01 1.49e+01 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 2402 16.57 - 33.13: 226 33.13 - 49.70: 58 49.70 - 66.27: 20 66.27 - 82.84: 6 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG A 73 " pdb=" CD ARG A 73 " pdb=" NE ARG A 73 " pdb=" CZ ARG A 73 " ideal model delta sinusoidal sigma weight residual 90.00 132.20 -42.20 2 1.50e+01 4.44e-03 9.62e+00 dihedral pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " pdb=" CD GLU A 130 " pdb=" OE1 GLU A 130 " ideal model delta sinusoidal sigma weight residual 0.00 82.84 -82.84 1 3.00e+01 1.11e-03 9.34e+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 82.78 -82.78 1 3.00e+01 1.11e-03 9.33e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 439 0.021 - 0.043: 91 0.043 - 0.064: 73 0.064 - 0.086: 31 0.086 - 0.107: 16 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -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 2.54 -0.10 2.00e-01 2.50e+01 2.59e-01 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 2.54 -0.10 2.00e-01 2.50e+01 2.55e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C HIS B 72 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS B 72 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 73 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 72 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C HIS A 72 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS A 72 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 73 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 41 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C LEU B 41 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU B 41 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 42 " 0.014 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.90: 1533 2.90 - 3.46: 4686 3.46 - 4.02: 7120 4.02 - 4.58: 10281 4.58 - 5.14: 13857 Nonbonded interactions: 37477 Sorted by model distance: nonbonded pdb=" O MET B 156 " pdb=" N MET B 159 " model vdw 2.337 3.120 nonbonded pdb=" O MET A 156 " pdb=" N MET A 159 " model vdw 2.338 3.120 nonbonded pdb=" NZ LYS B 144 " pdb=" O ASP B 153 " model vdw 2.365 3.120 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.365 3.120 nonbonded pdb=" O LYS A 42 " pdb=" C ALA A 43 " model vdw 2.403 3.270 ... (remaining 37472 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 group one per residue 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: 0.740 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: 0.030 Process input model: 6.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.004 0.076 4156 Z= 0.260 Angle : 0.502 7.563 5644 Z= 0.327 Chirality : 0.032 0.107 650 Planarity : 0.003 0.027 664 Dihedral : 14.128 82.835 1816 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.51 % 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: 4.91 (0.38), residues: 476 helix: 4.13 (0.24), residues: 380 sheet: None (None), residues: 0 loop : -0.92 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 3 TYR 0.004 0.000 TYR A 96 PHE 0.005 0.000 PHE A 109 TRP 0.002 0.000 TRP A 184 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4156) covalent geometry : angle 0.50172 ( 5644) hydrogen bonds : bond 0.12452 ( 331) hydrogen bonds : angle 4.41020 ( 969) *********************** 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 84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.166 Fit side-chains REVERT: A 47 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7343 (ttp80) REVERT: A 73 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7077 (ttp-170) REVERT: A 229 LEU cc_start: 0.6785 (mt) cc_final: 0.6348 (tt) REVERT: B 229 LEU cc_start: 0.6635 (mt) cc_final: 0.6383 (tt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1045 time to fit residues: 10.4396 Evaluate side-chains 76 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.135064 restraints weight = 4050.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.136307 restraints weight = 3712.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.137083 restraints weight = 3261.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137393 restraints weight = 3057.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.137601 restraints weight = 2979.116| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4156 Z= 0.139 Angle : 0.501 5.302 5644 Z= 0.270 Chirality : 0.036 0.110 650 Planarity : 0.003 0.027 664 Dihedral : 8.369 52.077 956 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.98 % Allowed : 9.07 % Favored : 89.95 % 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: 5.18 (0.38), residues: 476 helix: 4.17 (0.24), residues: 384 sheet: None (None), residues: 0 loop : -0.30 (0.74), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 36 TYR 0.010 0.001 TYR B 85 PHE 0.011 0.001 PHE B 223 TRP 0.006 0.001 TRP A 78 HIS 0.003 0.000 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4156) covalent geometry : angle 0.50061 ( 5644) hydrogen bonds : bond 0.03864 ( 331) hydrogen bonds : angle 3.35088 ( 969) *********************** 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 87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8585 (mm) cc_final: 0.8371 (mm) REVERT: A 47 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7298 (ttp80) REVERT: A 229 LEU cc_start: 0.7060 (mt) cc_final: 0.6472 (tt) REVERT: B 183 GLU cc_start: 0.8180 (tp30) cc_final: 0.7956 (mt-10) REVERT: B 229 LEU cc_start: 0.7054 (mt) cc_final: 0.6448 (tt) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.0904 time to fit residues: 9.3891 Evaluate side-chains 77 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL 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 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.164722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.122675 restraints weight = 4067.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.124003 restraints weight = 3505.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.124751 restraints weight = 3196.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.125647 restraints weight = 3023.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.125647 restraints weight = 2884.793| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4156 Z= 0.130 Angle : 0.509 8.474 5644 Z= 0.257 Chirality : 0.036 0.110 650 Planarity : 0.003 0.020 664 Dihedral : 7.647 52.257 952 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 3.43 % Allowed : 8.33 % Favored : 88.24 % 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: 5.17 (0.39), residues: 476 helix: 4.10 (0.23), residues: 390 sheet: None (None), residues: 0 loop : -0.36 (0.83), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.015 0.001 TYR B 85 PHE 0.010 0.001 PHE B 202 TRP 0.004 0.001 TRP A 78 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4156) covalent geometry : angle 0.50945 ( 5644) hydrogen bonds : bond 0.04306 ( 331) hydrogen bonds : angle 3.22689 ( 969) *********************** 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 93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.119 Fit side-chains REVERT: A 42 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7951 (tttt) REVERT: A 64 LEU cc_start: 0.8413 (tp) cc_final: 0.7900 (tp) REVERT: A 229 LEU cc_start: 0.7029 (mt) cc_final: 0.6486 (tt) REVERT: A 241 LEU cc_start: 0.8628 (tp) cc_final: 0.8358 (tt) REVERT: B 38 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 42 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7844 (tppp) REVERT: B 47 ARG cc_start: 0.8026 (tmm-80) cc_final: 0.7575 (ttp80) REVERT: B 64 LEU cc_start: 0.8476 (tp) cc_final: 0.7930 (tp) REVERT: B 182 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 183 GLU cc_start: 0.8213 (tp30) cc_final: 0.7822 (mt-10) REVERT: B 229 LEU cc_start: 0.7070 (mt) cc_final: 0.6500 (tt) REVERT: B 241 LEU cc_start: 0.8646 (tp) cc_final: 0.8375 (tt) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 0.1011 time to fit residues: 9.8535 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.164614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.120344 restraints weight = 4069.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.122000 restraints weight = 3432.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.122025 restraints weight = 3069.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.122025 restraints weight = 3061.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.122025 restraints weight = 3061.122| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4156 Z= 0.113 Angle : 0.469 6.031 5644 Z= 0.240 Chirality : 0.035 0.107 650 Planarity : 0.002 0.019 664 Dihedral : 7.261 53.528 952 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.70 % Allowed : 13.48 % 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: 5.15 (0.39), residues: 476 helix: 4.10 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.37 (0.83), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.011 0.001 TYR B 85 PHE 0.028 0.001 PHE A 202 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 4156) covalent geometry : angle 0.46855 ( 5644) hydrogen bonds : bond 0.04034 ( 331) hydrogen bonds : angle 3.12044 ( 969) *********************** 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 85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.6974 (mt) cc_final: 0.6395 (tt) REVERT: A 241 LEU cc_start: 0.8636 (tp) cc_final: 0.8406 (tt) REVERT: B 38 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: B 42 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7762 (tppp) REVERT: B 47 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7414 (ttp80) REVERT: B 57 GLU cc_start: 0.7554 (pm20) cc_final: 0.7197 (pm20) REVERT: B 182 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 183 GLU cc_start: 0.8045 (tp30) cc_final: 0.7821 (mt-10) REVERT: B 241 LEU cc_start: 0.8645 (tp) cc_final: 0.8427 (tt) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.1019 time to fit residues: 9.2933 Evaluate side-chains 77 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.158668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.114392 restraints weight = 4088.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115679 restraints weight = 3468.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.116795 restraints weight = 3154.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117432 restraints weight = 2945.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117432 restraints weight = 2822.930| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4156 Z= 0.142 Angle : 0.506 4.843 5644 Z= 0.262 Chirality : 0.037 0.112 650 Planarity : 0.002 0.017 664 Dihedral : 6.928 50.626 952 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.68 % Allowed : 14.46 % Favored : 81.86 % 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: 5.07 (0.39), residues: 476 helix: 4.03 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.39 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 245 TYR 0.014 0.001 TYR B 85 PHE 0.018 0.001 PHE A 202 TRP 0.003 0.001 TRP B 78 HIS 0.002 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4156) covalent geometry : angle 0.50598 ( 5644) hydrogen bonds : bond 0.04691 ( 331) hydrogen bonds : angle 3.18505 ( 969) *********************** 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 89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.146 Fit side-chains REVERT: A 182 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 229 LEU cc_start: 0.7046 (mt) cc_final: 0.6392 (tt) REVERT: A 241 LEU cc_start: 0.8671 (tp) cc_final: 0.8396 (tt) REVERT: B 47 ARG cc_start: 0.7912 (tmm-80) cc_final: 0.7684 (ttp80) REVERT: B 182 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8285 (mm-30) REVERT: B 241 LEU cc_start: 0.8673 (tp) cc_final: 0.8398 (tt) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0886 time to fit residues: 8.0927 Evaluate side-chains 73 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.156790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.114234 restraints weight = 4254.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.115041 restraints weight = 3776.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.115949 restraints weight = 3527.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.115949 restraints weight = 3351.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.115949 restraints weight = 3351.232| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4156 Z= 0.143 Angle : 0.515 4.868 5644 Z= 0.267 Chirality : 0.036 0.128 650 Planarity : 0.002 0.015 664 Dihedral : 6.713 49.131 952 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.68 % Allowed : 13.48 % 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 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: 4.86 (0.39), residues: 476 helix: 3.93 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.69 (0.80), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.012 0.001 TYR B 85 PHE 0.019 0.001 PHE A 246 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4156) covalent geometry : angle 0.51456 ( 5644) hydrogen bonds : bond 0.04688 ( 331) hydrogen bonds : angle 3.15356 ( 969) *********************** 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 83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.142 Fit side-chains REVERT: A 182 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 241 LEU cc_start: 0.8693 (tp) cc_final: 0.8321 (tt) REVERT: B 47 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7690 (ttp80) REVERT: B 182 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8096 (mm-30) REVERT: B 241 LEU cc_start: 0.8693 (tp) cc_final: 0.8319 (tt) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.0938 time to fit residues: 7.7936 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.155782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.112878 restraints weight = 4183.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.113778 restraints weight = 3706.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114681 restraints weight = 3450.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.115245 restraints weight = 3269.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.115260 restraints weight = 3140.134| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4156 Z= 0.135 Angle : 0.505 4.800 5644 Z= 0.264 Chirality : 0.036 0.115 650 Planarity : 0.002 0.015 664 Dihedral : 6.438 47.364 952 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.92 % Allowed : 13.97 % Favored : 82.11 % 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: 4.82 (0.39), residues: 476 helix: 3.92 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.76 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.011 0.001 TYR B 85 PHE 0.032 0.001 PHE B 202 TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4156) covalent geometry : angle 0.50499 ( 5644) hydrogen bonds : bond 0.04571 ( 331) hydrogen bonds : angle 3.12817 ( 969) *********************** 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 78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.092 Fit side-chains REVERT: A 36 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: A 182 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 182 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8182 (mm-30) REVERT: B 241 LEU cc_start: 0.8777 (tp) cc_final: 0.8426 (tt) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.0913 time to fit residues: 7.2909 Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.0170 overall best weight: 0.3830 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.159889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114861 restraints weight = 4102.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.116444 restraints weight = 3455.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.117579 restraints weight = 3105.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.117579 restraints weight = 2885.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.117579 restraints weight = 2885.172| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4156 Z= 0.109 Angle : 0.470 5.100 5644 Z= 0.246 Chirality : 0.034 0.116 650 Planarity : 0.002 0.018 664 Dihedral : 6.107 47.880 952 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 15.93 % Favored : 82.11 % 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: 4.95 (0.39), residues: 476 helix: 4.02 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.79 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.007 0.001 TYR B 85 PHE 0.025 0.001 PHE B 202 TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 4156) covalent geometry : angle 0.46987 ( 5644) hydrogen bonds : bond 0.03955 ( 331) hydrogen bonds : angle 3.02462 ( 969) *********************** 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 75 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.175 Fit side-chains REVERT: A 36 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7374 (mtp180) REVERT: A 241 LEU cc_start: 0.8753 (tp) cc_final: 0.8395 (tt) REVERT: B 182 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 241 LEU cc_start: 0.8749 (tp) cc_final: 0.8396 (tt) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.0828 time to fit residues: 6.9267 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 38 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.159270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.116272 restraints weight = 4161.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.117230 restraints weight = 3700.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.118071 restraints weight = 3425.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118294 restraints weight = 3240.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118294 restraints weight = 3174.320| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4156 Z= 0.113 Angle : 0.478 4.764 5644 Z= 0.253 Chirality : 0.035 0.119 650 Planarity : 0.002 0.020 664 Dihedral : 6.010 46.963 952 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 16.91 % Favored : 80.88 % 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: 4.94 (0.39), residues: 476 helix: 4.02 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.82 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.008 0.001 TYR B 85 PHE 0.027 0.001 PHE A 202 TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4156) covalent geometry : angle 0.47753 ( 5644) hydrogen bonds : bond 0.03958 ( 331) hydrogen bonds : angle 3.05381 ( 969) *********************** 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 73 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.156 Fit side-chains REVERT: A 36 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7398 (mtp180) REVERT: B 241 LEU cc_start: 0.8743 (tp) cc_final: 0.8414 (tt) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.0879 time to fit residues: 7.0412 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.153983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.108064 restraints weight = 4187.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.109231 restraints weight = 3656.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.109310 restraints weight = 3367.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110197 restraints weight = 3341.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.110635 restraints weight = 3167.521| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4156 Z= 0.221 Angle : 0.624 5.606 5644 Z= 0.330 Chirality : 0.040 0.140 650 Planarity : 0.003 0.025 664 Dihedral : 6.608 41.145 952 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 16.42 % Favored : 80.64 % 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: 4.58 (0.39), residues: 476 helix: 3.73 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.86 (0.77), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.018 0.001 TYR B 85 PHE 0.028 0.002 PHE B 202 TRP 0.005 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 4156) covalent geometry : angle 0.62355 ( 5644) hydrogen bonds : bond 0.05733 ( 331) hydrogen bonds : angle 3.34806 ( 969) ********************** 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 69 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.145 Fit side-chains REVERT: A 182 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 182 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8165 (mm-30) outliers start: 12 outliers final: 11 residues processed: 59 average time/residue: 0.0923 time to fit residues: 6.4742 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.154947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109239 restraints weight = 4143.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110511 restraints weight = 3581.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111494 restraints weight = 3267.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111494 restraints weight = 3073.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111494 restraints weight = 3073.414| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4156 Z= 0.129 Angle : 0.509 4.798 5644 Z= 0.270 Chirality : 0.036 0.131 650 Planarity : 0.003 0.024 664 Dihedral : 6.199 43.443 952 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 17.16 % Favored : 80.64 % 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: 4.62 (0.39), residues: 476 helix: 3.78 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.97 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 36 TYR 0.010 0.001 TYR B 85 PHE 0.028 0.001 PHE B 202 TRP 0.009 0.002 TRP B 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4156) covalent geometry : angle 0.50934 ( 5644) hydrogen bonds : bond 0.04693 ( 331) hydrogen bonds : angle 3.14280 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 793.51 seconds wall clock time: 14 minutes 19.98 seconds (859.98 seconds total)