Starting phenix.real_space_refine on Tue Feb 11 03:54:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1q_36799/02_2025/8k1q_36799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1q_36799/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1q_36799/02_2025/8k1q_36799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1q_36799/02_2025/8k1q_36799.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1q_36799/02_2025/8k1q_36799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1q_36799/02_2025/8k1q_36799.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.12, per 1000 atoms: 0.77 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: 1.03 Conformation dependent library (CDL) restraints added in 435.5 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 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: 1.18 Time building geometry restraints manager: 1.22 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 248 or resid 301 through 303)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.480 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.440 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- 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= 0.215 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.91 (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 TRP 0.002 0.000 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.005 0.000 PHE A 109 TYR 0.004 0.000 TYR A 96 ARG 0.001 0.000 ARG B 3 *********************** 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 : 0.428 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: 0.2164 time to fit residues: 21.6413 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 : 0.404 ------------------------------------------------------------------------------- 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 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.163245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118671 restraints weight = 4096.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.120226 restraints weight = 3423.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.121498 restraints weight = 3066.867| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4156 Z= 0.264 Angle : 0.570 4.981 5644 Z= 0.309 Chirality : 0.039 0.119 650 Planarity : 0.003 0.025 664 Dihedral : 8.328 52.766 956 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.96 % Allowed : 9.31 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.38), residues: 476 helix: 3.86 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.57 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.002 PHE B 223 TYR 0.020 0.002 TYR B 85 ARG 0.009 0.001 ARG A 36 *********************** 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 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7032 (tpp) REVERT: A 183 GLU cc_start: 0.8253 (tp30) cc_final: 0.8004 (mt-10) REVERT: A 229 LEU cc_start: 0.7058 (mt) cc_final: 0.6421 (tt) REVERT: A 241 LEU cc_start: 0.8563 (tp) cc_final: 0.8314 (tt) REVERT: B 42 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7970 (ttpt) REVERT: B 168 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7067 (tpp) REVERT: B 183 GLU cc_start: 0.8297 (tp30) cc_final: 0.7950 (mt-10) REVERT: B 229 LEU cc_start: 0.7095 (mt) cc_final: 0.6433 (tt) REVERT: B 241 LEU cc_start: 0.8558 (tp) cc_final: 0.8281 (tt) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1779 time to fit residues: 19.8563 Evaluate side-chains 83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 MET 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 168 MET Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.163480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120367 restraints weight = 4051.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.121796 restraints weight = 3508.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.122757 restraints weight = 3202.402| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4156 Z= 0.165 Angle : 0.509 8.579 5644 Z= 0.257 Chirality : 0.036 0.132 650 Planarity : 0.003 0.025 664 Dihedral : 7.757 51.232 952 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.19 % Allowed : 12.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.39), residues: 476 helix: 3.99 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.41 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 PHE 0.028 0.001 PHE A 202 TYR 0.012 0.001 TYR B 85 ARG 0.006 0.001 ARG A 47 *********************** 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 96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7910 (ttpt) REVERT: A 182 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 183 GLU cc_start: 0.8138 (tp30) cc_final: 0.7829 (mt-10) REVERT: A 229 LEU cc_start: 0.7023 (mt) cc_final: 0.6424 (tt) REVERT: A 241 LEU cc_start: 0.8585 (tp) cc_final: 0.8319 (tt) REVERT: B 47 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7674 (ttp80) REVERT: B 64 LEU cc_start: 0.8526 (mt) cc_final: 0.8068 (tp) REVERT: B 183 GLU cc_start: 0.8162 (tp30) cc_final: 0.7768 (mt-10) REVERT: B 229 LEU cc_start: 0.7067 (mt) cc_final: 0.6464 (tt) REVERT: B 241 LEU cc_start: 0.8601 (tp) cc_final: 0.8338 (tt) outliers start: 13 outliers final: 5 residues processed: 85 average time/residue: 0.2159 time to fit residues: 21.8696 Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 158 ASN B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.118415 restraints weight = 4095.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119830 restraints weight = 3420.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.121272 restraints weight = 3080.895| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4156 Z= 0.152 Angle : 0.471 5.862 5644 Z= 0.242 Chirality : 0.035 0.115 650 Planarity : 0.002 0.017 664 Dihedral : 7.359 52.375 952 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 14.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.39), residues: 476 helix: 4.00 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.47 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 PHE 0.017 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.005 0.001 ARG B 131 *********************** 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 94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7487 (tppt) REVERT: A 183 GLU cc_start: 0.8071 (tp30) cc_final: 0.7841 (mt-10) REVERT: A 209 GLN cc_start: 0.7278 (pp30) cc_final: 0.7026 (pp30) REVERT: A 229 LEU cc_start: 0.7013 (mt) cc_final: 0.6412 (tt) REVERT: A 241 LEU cc_start: 0.8588 (tp) cc_final: 0.8305 (tt) REVERT: B 45 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 47 ARG cc_start: 0.8148 (tmm-80) cc_final: 0.7435 (ttp80) REVERT: B 64 LEU cc_start: 0.8521 (mt) cc_final: 0.8300 (tp) REVERT: B 183 GLU cc_start: 0.8054 (tp30) cc_final: 0.7781 (mt-10) REVERT: B 241 LEU cc_start: 0.8606 (tp) cc_final: 0.8321 (tt) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.1981 time to fit residues: 20.5740 Evaluate side-chains 74 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.160245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.116776 restraints weight = 4201.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.117603 restraints weight = 3664.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.118769 restraints weight = 3393.213| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4156 Z= 0.172 Angle : 0.493 5.146 5644 Z= 0.254 Chirality : 0.036 0.112 650 Planarity : 0.002 0.014 664 Dihedral : 7.003 51.071 952 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.21 % Allowed : 16.42 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.92 (0.39), residues: 476 helix: 3.95 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.54 (0.79), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.001 0.000 HIS B 98 PHE 0.027 0.001 PHE A 202 TYR 0.011 0.001 TYR A 85 ARG 0.002 0.000 ARG B 131 *********************** 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 88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7893 (tppp) REVERT: A 209 GLN cc_start: 0.7334 (pp30) cc_final: 0.7076 (pp30) REVERT: A 241 LEU cc_start: 0.8689 (tp) cc_final: 0.8397 (tt) REVERT: B 36 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: B 47 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7768 (ttp80) REVERT: B 241 LEU cc_start: 0.8695 (tp) cc_final: 0.8403 (tt) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.2275 time to fit residues: 21.5797 Evaluate side-chains 76 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 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 = 0.3632 r_free = 0.3632 target = 0.158911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114190 restraints weight = 4116.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115637 restraints weight = 3522.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.116630 restraints weight = 3186.062| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4156 Z= 0.186 Angle : 0.498 4.808 5644 Z= 0.258 Chirality : 0.035 0.116 650 Planarity : 0.002 0.014 664 Dihedral : 6.697 50.259 952 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.94 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.39), residues: 476 helix: 3.94 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.76 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS B 98 PHE 0.022 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.003 0.000 ARG A 131 *********************** 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 82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.401 Fit side-chains REVERT: A 182 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 241 LEU cc_start: 0.8666 (tp) cc_final: 0.8367 (tt) REVERT: B 36 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7358 (mtm-85) REVERT: B 45 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 182 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 241 LEU cc_start: 0.8654 (tp) cc_final: 0.8332 (tt) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.1954 time to fit residues: 17.1390 Evaluate side-chains 74 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 136 VAL 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 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.160015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116981 restraints weight = 4113.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.117887 restraints weight = 3634.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.118517 restraints weight = 3377.368| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4156 Z= 0.138 Angle : 0.467 4.775 5644 Z= 0.246 Chirality : 0.034 0.116 650 Planarity : 0.002 0.020 664 Dihedral : 6.416 50.380 952 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 16.42 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.90 (0.39), residues: 476 helix: 3.98 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.75 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS B 98 PHE 0.020 0.001 PHE A 202 TYR 0.007 0.001 TYR B 85 ARG 0.003 0.000 ARG A 131 *********************** 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 75 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.419 Fit side-chains REVERT: A 36 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7438 (mtm-85) REVERT: A 209 GLN cc_start: 0.7480 (mm110) cc_final: 0.7163 (pp30) REVERT: A 241 LEU cc_start: 0.8689 (tp) cc_final: 0.8411 (tt) REVERT: B 36 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7394 (mtp180) REVERT: B 182 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 241 LEU cc_start: 0.8713 (tp) cc_final: 0.8380 (tt) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.2082 time to fit residues: 17.2349 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.157470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.114360 restraints weight = 4117.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.115253 restraints weight = 3681.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.116080 restraints weight = 3436.478| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.183 Angle : 0.509 5.629 5644 Z= 0.269 Chirality : 0.035 0.127 650 Planarity : 0.002 0.016 664 Dihedral : 6.341 47.916 952 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 17.65 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.39), residues: 476 helix: 3.95 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.88 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.021 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.002 0.000 ARG A 131 *********************** 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 79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.466 Fit side-chains REVERT: A 36 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7417 (mtp180) REVERT: A 209 GLN cc_start: 0.7633 (mm110) cc_final: 0.7323 (pp30) REVERT: A 241 LEU cc_start: 0.8785 (tp) cc_final: 0.8426 (tt) REVERT: B 36 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7466 (mtp180) REVERT: B 64 LEU cc_start: 0.8596 (tp) cc_final: 0.8067 (tp) REVERT: B 241 LEU cc_start: 0.8777 (tp) cc_final: 0.8411 (tt) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1944 time to fit residues: 16.7556 Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.114497 restraints weight = 4191.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115556 restraints weight = 3732.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116433 restraints weight = 3450.200| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4156 Z= 0.173 Angle : 0.500 5.988 5644 Z= 0.265 Chirality : 0.035 0.129 650 Planarity : 0.002 0.016 664 Dihedral : 6.129 46.554 952 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 17.65 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.38), residues: 476 helix: 3.87 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.67 (0.77), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.020 0.001 PHE A 202 TYR 0.009 0.001 TYR B 85 ARG 0.002 0.000 ARG A 131 *********************** 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: 10 poor density : 63 time to evaluate : 0.397 Fit side-chains REVERT: A 36 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7424 (mtp180) REVERT: A 209 GLN cc_start: 0.7754 (mm110) cc_final: 0.7385 (pp30) REVERT: A 241 LEU cc_start: 0.8786 (tp) cc_final: 0.8452 (tt) REVERT: B 36 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7443 (mtp180) REVERT: B 182 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 241 LEU cc_start: 0.8772 (tp) cc_final: 0.8438 (tt) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.2045 time to fit residues: 16.0521 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 136 VAL 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 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.152767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.108847 restraints weight = 4241.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.109631 restraints weight = 3872.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110187 restraints weight = 3646.079| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4156 Z= 0.258 Angle : 0.573 6.597 5644 Z= 0.303 Chirality : 0.038 0.136 650 Planarity : 0.002 0.015 664 Dihedral : 6.375 42.803 952 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.38), residues: 476 helix: 3.83 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.93 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.021 0.001 PHE A 202 TYR 0.013 0.001 TYR B 85 ARG 0.002 0.000 ARG A 47 ********************** 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 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.444 Fit side-chains REVERT: A 36 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7594 (mtp180) REVERT: A 209 GLN cc_start: 0.7844 (mm110) cc_final: 0.7600 (mm-40) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.2063 time to fit residues: 15.9225 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.154288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.108554 restraints weight = 4167.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.109621 restraints weight = 3612.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.110634 restraints weight = 3322.958| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.197 Angle : 0.525 6.141 5644 Z= 0.278 Chirality : 0.036 0.133 650 Planarity : 0.002 0.017 664 Dihedral : 6.222 43.512 952 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.38), residues: 476 helix: 3.81 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.93 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.020 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.002 0.000 ARG B 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1371.69 seconds wall clock time: 25 minutes 19.48 seconds (1519.48 seconds total)