Starting phenix.real_space_refine on Wed Mar 5 22:20:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.map" model { file = "/net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xos_33358/03_2025/7xos_33358.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 3.50, per 1000 atoms: 0.91 Number of scatterers: 3855 At special positions: 0 Unit cell: (73.08, 88.74, 69.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 773 8.00 N 665 7.00 C 2397 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: 1.04 Conformation dependent library (CDL) restraints added in 530.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 59.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'K' and resid 9 through 28 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.805A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.700A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.630A pdb=" N LEU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 268 removed outlier: 4.086A pdb=" N ALA K 260 " --> pdb=" O GLY K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.863A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.299A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 459 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 4.131A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.268A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'K' and resid 476 through 479 262 hydrogen bonds defined for protein. 756 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: 1.16 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1312 1.34 - 1.45: 243 1.45 - 1.57: 2291 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CG1 ILE K 353 " pdb=" CD1 ILE K 353 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CA ALA K 449 " pdb=" C ALA K 449 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.60e-01 bond pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.40e-02 5.10e+03 5.32e-01 bond pdb=" C VAL K 169 " pdb=" O VAL K 169 " ideal model delta sigma weight residual 1.230 1.242 -0.013 1.78e-02 3.16e+03 5.14e-01 bond pdb=" C VAL K 27 " pdb=" O VAL K 27 " ideal model delta sigma weight residual 1.241 1.233 0.007 1.03e-02 9.43e+03 5.09e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5071 1.41 - 2.81: 139 2.81 - 4.22: 25 4.22 - 5.62: 6 5.62 - 7.03: 2 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N ILE K 305 " pdb=" CA ILE K 305 " pdb=" C ILE K 305 " ideal model delta sigma weight residual 112.80 109.43 3.37 1.15e+00 7.56e-01 8.58e+00 angle pdb=" N GLN K 351 " pdb=" CA GLN K 351 " pdb=" CB GLN K 351 " ideal model delta sigma weight residual 110.22 114.64 -4.42 1.54e+00 4.22e-01 8.24e+00 angle pdb=" N GLU K 164 " pdb=" CA GLU K 164 " pdb=" CB GLU K 164 " ideal model delta sigma weight residual 110.39 114.81 -4.42 1.66e+00 3.63e-01 7.10e+00 angle pdb=" C VAL K 169 " pdb=" CA VAL K 169 " pdb=" CB VAL K 169 " ideal model delta sigma weight residual 112.46 109.49 2.97 1.33e+00 5.65e-01 4.99e+00 angle pdb=" CA LEU K 234 " pdb=" C LEU K 234 " pdb=" N PRO K 235 " ideal model delta sigma weight residual 118.44 121.95 -3.51 1.59e+00 3.96e-01 4.87e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 2135 15.94 - 31.89: 224 31.89 - 47.83: 48 47.83 - 63.78: 2 63.78 - 79.72: 3 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA GLU K 354 " pdb=" C GLU K 354 " pdb=" N GLU K 355 " pdb=" CA GLU K 355 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PHE K 219 " pdb=" C PHE K 219 " pdb=" N ILE K 220 " pdb=" CA ILE K 220 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N LYS K 321 " pdb=" CA LYS K 321 " pdb=" CB LYS K 321 " pdb=" CG LYS K 321 " ideal model delta sinusoidal sigma weight residual -60.00 -112.99 52.99 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 394 0.028 - 0.057: 154 0.057 - 0.085: 49 0.085 - 0.113: 31 0.113 - 0.142: 10 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU K 164 " pdb=" N GLU K 164 " pdb=" C GLU K 164 " pdb=" CB GLU K 164 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA GLN K 72 " pdb=" N GLN K 72 " pdb=" C GLN K 72 " pdb=" CB GLN K 72 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA GLU K 354 " pdb=" N GLU K 354 " pdb=" C GLU K 354 " pdb=" CB GLU K 354 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 160 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C LYS K 160 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS K 160 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU K 161 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 161 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU K 161 " -0.021 2.00e-02 2.50e+03 pdb=" O LEU K 161 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE K 162 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 234 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO K 235 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO K 235 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 235 " -0.016 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 65 2.67 - 3.23: 3838 3.23 - 3.78: 6356 3.78 - 4.34: 7900 4.34 - 4.90: 13141 Nonbonded interactions: 31300 Sorted by model distance: nonbonded pdb=" OG1 THR K 385 " pdb=" OE1 GLU K 388 " model vdw 2.109 3.040 nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.152 3.040 nonbonded pdb=" O GLY K 173 " pdb=" NH2 ARG K 404 " model vdw 2.175 3.120 nonbonded pdb=" OG SER K 228 " pdb=" OE2 GLU K 255 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR K 296 " pdb=" O GLN K 319 " model vdw 2.249 3.040 ... (remaining 31295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.003 0.042 3883 Z= 0.193 Angle : 0.578 7.027 5243 Z= 0.344 Chirality : 0.041 0.142 638 Planarity : 0.003 0.027 687 Dihedral : 13.124 79.720 1464 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.36), residues: 522 helix: 1.78 (0.30), residues: 295 sheet: 0.83 (0.65), residues: 70 loop : -0.72 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.010 0.001 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.002 0.000 ARG K 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4353 (pp20) cc_final: 0.3516 (pt0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1346 time to fit residues: 8.9157 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.097811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069422 restraints weight = 11476.038| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.77 r_work: 0.3173 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3883 Z= 0.289 Angle : 0.630 10.790 5243 Z= 0.329 Chirality : 0.043 0.147 638 Planarity : 0.004 0.046 687 Dihedral : 4.144 19.686 552 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.49 % Allowed : 9.41 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.35), residues: 522 helix: 1.83 (0.30), residues: 297 sheet: 0.81 (0.62), residues: 70 loop : -0.92 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.016 0.002 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.004 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.482 Fit side-chains REVERT: K 61 GLU cc_start: 0.4916 (pp20) cc_final: 0.4020 (pt0) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1478 time to fit residues: 8.1947 Evaluate side-chains 34 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 281 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.096704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068289 restraints weight = 11606.261| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.83 r_work: 0.3135 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3883 Z= 0.327 Angle : 0.614 9.596 5243 Z= 0.320 Chirality : 0.043 0.147 638 Planarity : 0.003 0.038 687 Dihedral : 4.189 17.227 552 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.72 % Allowed : 10.15 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.35), residues: 522 helix: 1.78 (0.29), residues: 297 sheet: 0.70 (0.62), residues: 70 loop : -0.98 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.012 0.002 PHE K 195 TYR 0.009 0.001 TYR K 506 ARG 0.004 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5551 (pp20) cc_final: 0.4459 (pt0) REVERT: K 351 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7755 (pp30) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.1549 time to fit residues: 8.8109 Evaluate side-chains 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.0770 chunk 26 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 35 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.098079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070122 restraints weight = 11660.500| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.90 r_work: 0.3170 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.189 Angle : 0.552 10.380 5243 Z= 0.282 Chirality : 0.040 0.139 638 Planarity : 0.003 0.030 687 Dihedral : 3.985 16.663 552 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.23 % Allowed : 11.63 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.35), residues: 522 helix: 2.04 (0.29), residues: 297 sheet: 0.74 (0.62), residues: 70 loop : -0.91 (0.43), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.008 0.001 TYR K 476 ARG 0.003 0.000 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.473 Fit side-chains REVERT: K 61 GLU cc_start: 0.5567 (pp20) cc_final: 0.4421 (pt0) REVERT: K 267 MET cc_start: 0.5691 (mmt) cc_final: 0.5375 (mmt) REVERT: K 308 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7560 (mm-30) REVERT: K 351 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8217 (pm20) outliers start: 9 outliers final: 4 residues processed: 43 average time/residue: 0.1859 time to fit residues: 10.2069 Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 401 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.098335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070717 restraints weight = 11850.550| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.86 r_work: 0.3195 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3883 Z= 0.153 Angle : 0.543 10.210 5243 Z= 0.275 Chirality : 0.040 0.140 638 Planarity : 0.003 0.020 687 Dihedral : 3.887 15.827 552 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.22 % Allowed : 12.13 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.35), residues: 522 helix: 2.16 (0.29), residues: 297 sheet: 1.00 (0.63), residues: 64 loop : -0.90 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.011 0.001 TYR K 506 ARG 0.001 0.000 ARG K 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5225 (pp20) cc_final: 0.4053 (pt0) REVERT: K 267 MET cc_start: 0.5672 (mmt) cc_final: 0.5345 (mmt) REVERT: K 351 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7967 (pm20) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 0.1470 time to fit residues: 8.7999 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.098601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070921 restraints weight = 11701.044| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.86 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3883 Z= 0.159 Angle : 0.571 11.303 5243 Z= 0.282 Chirality : 0.040 0.148 638 Planarity : 0.002 0.020 687 Dihedral : 3.835 16.688 552 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.49 % Allowed : 13.61 % Favored : 84.90 % 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: 1.75 (0.36), residues: 522 helix: 2.23 (0.29), residues: 297 sheet: 0.68 (0.62), residues: 70 loop : -0.75 (0.44), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.001 PHE K 195 TYR 0.009 0.001 TYR K 476 ARG 0.001 0.000 ARG K 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5079 (pp20) cc_final: 0.3961 (pt0) REVERT: K 267 MET cc_start: 0.5720 (mmt) cc_final: 0.5383 (mmt) REVERT: K 351 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8187 (pm20) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.1479 time to fit residues: 7.8925 Evaluate side-chains 36 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 401 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.097601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069686 restraints weight = 11890.286| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.92 r_work: 0.3164 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3883 Z= 0.231 Angle : 0.605 12.531 5243 Z= 0.300 Chirality : 0.042 0.152 638 Planarity : 0.003 0.020 687 Dihedral : 3.947 17.924 552 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.48 % Allowed : 15.10 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.36), residues: 522 helix: 2.18 (0.29), residues: 297 sheet: 0.57 (0.62), residues: 70 loop : -0.75 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.008 0.001 TYR K 476 ARG 0.002 0.000 ARG K 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5225 (pp20) cc_final: 0.4078 (pt0) REVERT: K 267 MET cc_start: 0.5806 (mmt) cc_final: 0.5514 (mmt) REVERT: K 351 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8179 (pm20) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.1379 time to fit residues: 7.2888 Evaluate side-chains 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.0000 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 overall best weight: 0.5946 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.098756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071228 restraints weight = 11848.973| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.92 r_work: 0.3213 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3883 Z= 0.149 Angle : 0.591 12.398 5243 Z= 0.291 Chirality : 0.041 0.147 638 Planarity : 0.002 0.017 687 Dihedral : 3.822 22.023 552 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.72 % Allowed : 14.60 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.36), residues: 522 helix: 2.33 (0.29), residues: 297 sheet: 0.63 (0.60), residues: 78 loop : -0.72 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.013 0.001 PHE K 195 TYR 0.010 0.001 TYR K 476 ARG 0.001 0.000 ARG K 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4811 (pp20) cc_final: 0.3849 (pt0) REVERT: K 72 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8349 (mp-120) REVERT: K 193 MET cc_start: 0.6362 (ppp) cc_final: 0.5144 (ppp) REVERT: K 267 MET cc_start: 0.5833 (mmt) cc_final: 0.5531 (mmt) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.1415 time to fit residues: 9.0168 Evaluate side-chains 40 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 232 GLU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 overall best weight: 1.3364 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.098546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071023 restraints weight = 11848.412| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.90 r_work: 0.3207 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3883 Z= 0.177 Angle : 0.662 12.053 5243 Z= 0.325 Chirality : 0.041 0.145 638 Planarity : 0.003 0.020 687 Dihedral : 3.866 21.809 552 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.23 % Allowed : 15.59 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.36), residues: 522 helix: 2.28 (0.29), residues: 297 sheet: 0.48 (0.59), residues: 78 loop : -0.74 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.015 0.002 PHE K 195 TYR 0.010 0.001 TYR K 485 ARG 0.001 0.000 ARG K 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4919 (pp20) cc_final: 0.3970 (pt0) REVERT: K 72 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8367 (mp-120) REVERT: K 267 MET cc_start: 0.5850 (mmt) cc_final: 0.5548 (mmt) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.1500 time to fit residues: 7.8107 Evaluate side-chains 38 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 232 GLU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.098709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.070946 restraints weight = 11635.266| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.84 r_work: 0.3203 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3883 Z= 0.193 Angle : 0.654 11.851 5243 Z= 0.324 Chirality : 0.041 0.158 638 Planarity : 0.003 0.022 687 Dihedral : 3.883 21.479 552 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.73 % Allowed : 16.09 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.36), residues: 522 helix: 2.27 (0.29), residues: 297 sheet: 0.41 (0.60), residues: 78 loop : -0.75 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.010 0.001 TYR K 485 ARG 0.001 0.000 ARG K 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4992 (pp20) cc_final: 0.3922 (pt0) REVERT: K 72 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8412 (mp-120) REVERT: K 267 MET cc_start: 0.5832 (mmt) cc_final: 0.5523 (mmt) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.1629 time to fit residues: 7.9929 Evaluate side-chains 39 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 232 GLU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 388 GLU Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 30.0000 chunk 20 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.099365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072182 restraints weight = 11607.174| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.89 r_work: 0.3233 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3883 Z= 0.160 Angle : 0.631 11.597 5243 Z= 0.312 Chirality : 0.041 0.139 638 Planarity : 0.003 0.020 687 Dihedral : 3.817 22.479 552 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.72 % Allowed : 15.10 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.36), residues: 522 helix: 2.26 (0.29), residues: 299 sheet: 0.40 (0.60), residues: 78 loop : -0.67 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.010 0.001 TYR K 485 ARG 0.001 0.000 ARG K 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.43 seconds wall clock time: 39 minutes 3.21 seconds (2343.21 seconds total)