Starting phenix.real_space_refine on Sun Mar 10 18:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_33358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_33358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_33358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_33358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xos_33358/03_2024/7xos_33358.pdb" } 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 Residue "K GLU 102": "OE1" <-> "OE2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 316": "OD1" <-> "OD2" Residue "K TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.41, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.34 Conformation dependent library (CDL) restraints added in 777.9 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: 0.39 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: 1.08 Time building geometry restraints manager: 1.49 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: 99.98 - 106.19: 71 106.19 - 112.41: 2062 112.41 - 118.62: 1138 118.62 - 124.84: 1957 124.84 - 131.05: 15 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 2.440 nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.152 2.440 nonbonded pdb=" O GLY K 173 " pdb=" NH2 ARG K 404 " model vdw 2.175 2.520 nonbonded pdb=" OG SER K 228 " pdb=" OE2 GLU K 255 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR K 296 " pdb=" O GLN K 319 " model vdw 2.249 2.440 ... (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: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 5.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.100 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.450 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: 0.1377 time to fit residues: 9.1065 Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3883 Z= 0.336 Angle : 0.640 10.480 5243 Z= 0.333 Chirality : 0.044 0.142 638 Planarity : 0.003 0.021 687 Dihedral : 4.173 19.503 552 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.49 % Allowed : 10.40 % Favored : 88.12 % 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: 1.28 (0.36), residues: 522 helix: 1.79 (0.29), residues: 297 sheet: 0.62 (0.61), residues: 78 loop : -0.98 (0.43), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.017 0.002 PHE K 195 TYR 0.006 0.001 TYR K 478 ARG 0.003 0.000 ARG K 452 *********************** 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 fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.456 Fit side-chains REVERT: K 61 GLU cc_start: 0.4644 (pp20) cc_final: 0.3761 (pt0) outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1465 time to fit residues: 8.0734 Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 39 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3883 Z= 0.219 Angle : 0.560 10.222 5243 Z= 0.288 Chirality : 0.041 0.140 638 Planarity : 0.003 0.024 687 Dihedral : 3.968 14.054 552 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.98 % Allowed : 11.39 % Favored : 86.63 % 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: 1.51 (0.36), residues: 522 helix: 2.02 (0.29), residues: 297 sheet: 0.72 (0.60), residues: 78 loop : -0.96 (0.44), 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 0.009 0.001 TYR K 506 ARG 0.001 0.000 ARG K 452 *********************** 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 43 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.464 Fit side-chains REVERT: K 61 GLU cc_start: 0.4919 (pp20) cc_final: 0.4560 (pp20) REVERT: K 267 MET cc_start: 0.5407 (mmt) cc_final: 0.5151 (mmt) outliers start: 8 outliers final: 4 residues processed: 39 average time/residue: 0.1563 time to fit residues: 8.2133 Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE 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 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3883 Z= 0.173 Angle : 0.533 10.194 5243 Z= 0.270 Chirality : 0.040 0.139 638 Planarity : 0.002 0.017 687 Dihedral : 3.846 14.006 552 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.23 % Allowed : 12.13 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.36), residues: 522 helix: 2.13 (0.29), residues: 297 sheet: 0.75 (0.60), residues: 78 loop : -0.91 (0.45), 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 0.007 0.001 TYR K 478 ARG 0.001 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 43 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.468 Fit side-chains REVERT: K 61 GLU cc_start: 0.5006 (pp20) cc_final: 0.4041 (pt0) REVERT: K 267 MET cc_start: 0.5431 (mmt) cc_final: 0.5179 (mmt) REVERT: K 308 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7372 (mm-30) REVERT: K 351 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8138 (mp10) outliers start: 9 outliers final: 3 residues processed: 41 average time/residue: 0.1379 time to fit residues: 7.7204 Evaluate side-chains 37 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 37 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3883 Z= 0.261 Angle : 0.581 10.681 5243 Z= 0.295 Chirality : 0.041 0.148 638 Planarity : 0.003 0.023 687 Dihedral : 3.978 15.614 552 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.23 % Allowed : 14.11 % Favored : 83.66 % 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: 1.60 (0.35), residues: 522 helix: 2.11 (0.29), residues: 297 sheet: 0.98 (0.64), residues: 66 loop : -0.95 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.007 0.001 TYR K 478 ARG 0.002 0.000 ARG K 452 *********************** 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 41 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.376 Fit side-chains REVERT: K 61 GLU cc_start: 0.5163 (pp20) cc_final: 0.4699 (pp20) REVERT: K 518 GLU cc_start: 0.5551 (pt0) cc_final: 0.5349 (pt0) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.1174 time to fit residues: 6.2589 Evaluate side-chains 36 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 73 MET 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 401 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3883 Z= 0.346 Angle : 0.631 9.407 5243 Z= 0.323 Chirality : 0.043 0.149 638 Planarity : 0.003 0.026 687 Dihedral : 4.129 16.668 552 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.22 % Allowed : 13.61 % Favored : 83.17 % 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: 1.41 (0.35), residues: 522 helix: 1.93 (0.29), residues: 297 sheet: 1.21 (0.65), residues: 60 loop : -1.05 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.008 0.001 TYR K 478 ARG 0.002 0.000 ARG K 452 *********************** 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 46 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5121 (pp20) cc_final: 0.4142 (pt0) REVERT: K 518 GLU cc_start: 0.5461 (pt0) cc_final: 0.5217 (pt0) outliers start: 13 outliers final: 10 residues processed: 44 average time/residue: 0.1374 time to fit residues: 8.1050 Evaluate side-chains 42 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3883 Z= 0.283 Angle : 0.612 10.191 5243 Z= 0.311 Chirality : 0.042 0.142 638 Planarity : 0.003 0.021 687 Dihedral : 4.138 17.078 552 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.22 % Allowed : 14.60 % 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: 1.41 (0.36), residues: 522 helix: 1.91 (0.29), residues: 297 sheet: 0.56 (0.63), residues: 70 loop : -0.81 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.014 0.002 PHE K 195 TYR 0.008 0.001 TYR K 478 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 46 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.5096 (pp20) cc_final: 0.4125 (pt0) REVERT: K 518 GLU cc_start: 0.5434 (pt0) cc_final: 0.5215 (pt0) outliers start: 13 outliers final: 9 residues processed: 44 average time/residue: 0.1260 time to fit residues: 7.6569 Evaluate side-chains 40 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 281 PHE 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 24 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3883 Z= 0.215 Angle : 0.600 10.817 5243 Z= 0.301 Chirality : 0.042 0.180 638 Planarity : 0.003 0.019 687 Dihedral : 4.090 18.457 552 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 3.71 % Allowed : 14.60 % Favored : 81.68 % 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: 1.47 (0.36), residues: 522 helix: 2.05 (0.29), residues: 296 sheet: 0.47 (0.60), residues: 78 loop : -0.97 (0.47), residues: 148 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 0.007 0.001 TYR K 478 ARG 0.001 0.000 ARG K 285 *********************** 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 47 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4759 (pp20) cc_final: 0.3817 (pt0) REVERT: K 518 GLU cc_start: 0.5250 (pt0) cc_final: 0.5017 (pt0) outliers start: 15 outliers final: 11 residues processed: 45 average time/residue: 0.1255 time to fit residues: 7.7723 Evaluate side-chains 43 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 234 LEU 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 401 HIS 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 42 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3883 Z= 0.152 Angle : 0.573 11.233 5243 Z= 0.284 Chirality : 0.040 0.143 638 Planarity : 0.002 0.017 687 Dihedral : 3.908 20.835 552 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.98 % Allowed : 16.58 % Favored : 81.44 % 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: 1.73 (0.36), residues: 522 helix: 2.30 (0.29), residues: 296 sheet: 0.51 (0.61), residues: 78 loop : -0.92 (0.46), residues: 148 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 0.001 0.000 ARG K 501 *********************** 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 43 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: K 61 GLU cc_start: 0.4692 (pp20) cc_final: 0.3734 (pt0) REVERT: K 72 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: K 193 MET cc_start: 0.6689 (ppp) cc_final: 0.5442 (ppp) REVERT: K 518 GLU cc_start: 0.5710 (pt0) cc_final: 0.5364 (pt0) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1454 time to fit residues: 8.1282 Evaluate side-chains 40 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 401 HIS 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 31 optimal weight: 30.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3883 Z= 0.190 Angle : 0.596 12.363 5243 Z= 0.291 Chirality : 0.041 0.149 638 Planarity : 0.002 0.019 687 Dihedral : 3.900 20.566 552 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.73 % Allowed : 16.58 % Favored : 81.68 % 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: 1.74 (0.36), residues: 522 helix: 2.31 (0.29), residues: 296 sheet: 0.47 (0.61), residues: 78 loop : -0.90 (0.46), residues: 148 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 0.001 0.000 ARG K 404 ********************** 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 fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.413 Fit side-chains REVERT: K 61 GLU cc_start: 0.4687 (pp20) cc_final: 0.3794 (pt0) REVERT: K 72 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: K 518 GLU cc_start: 0.5466 (pt0) cc_final: 0.5266 (pt0) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1320 time to fit residues: 6.7206 Evaluate side-chains 38 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 401 HIS 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 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.099159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071577 restraints weight = 11708.489| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.91 r_work: 0.3210 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3883 Z= 0.135 Angle : 0.581 12.358 5243 Z= 0.280 Chirality : 0.040 0.148 638 Planarity : 0.002 0.017 687 Dihedral : 3.784 20.629 552 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.98 % Allowed : 16.83 % Favored : 81.19 % 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: 1.93 (0.36), residues: 522 helix: 2.50 (0.29), residues: 290 sheet: 0.51 (0.60), residues: 78 loop : -0.72 (0.45), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS K 401 PHE 0.013 0.001 PHE K 195 TYR 0.008 0.001 TYR K 476 ARG 0.002 0.000 ARG K 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.67 seconds wall clock time: 20 minutes 48.26 seconds (1248.26 seconds total)