Starting phenix.real_space_refine on Wed Feb 12 13:54:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.map" model { file = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uk5_26575/02_2025/7uk5_26575.cif" } resolution = 2.76 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= 0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.50, per 1000 atoms: 0.56 Number of scatterers: 8000 At special positions: 0 Unit cell: (116.466, 116.466, 78.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.096A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 Processing helix chain 'D' and resid 401 through 424 633 hydrogen bonds defined for protein. 1815 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: 2.25 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 2009 1.46 - 1.58: 3655 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" C GLN C 417 " pdb=" N ARG C 418 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.98e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10372 1.00 - 1.99: 585 1.99 - 2.99: 115 2.99 - 3.98: 33 3.98 - 4.98: 19 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.67e+00 angle pdb=" N THR B 182 " pdb=" CA THR B 182 " pdb=" C THR B 182 " ideal model delta sigma weight residual 113.41 110.51 2.90 1.22e+00 6.72e-01 5.66e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.41 110.53 2.88 1.22e+00 6.72e-01 5.58e+00 angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4400 17.87 - 35.73: 336 35.73 - 53.60: 44 53.60 - 71.47: 4 71.47 - 89.34: 8 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.89 -43.11 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 702 0.027 - 0.055: 352 0.055 - 0.082: 199 0.082 - 0.110: 41 0.110 - 0.137: 26 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN B 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN A 417 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 417 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 418 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN C 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN C 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 418 " 0.019 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 810 2.74 - 3.34: 10002 3.34 - 3.94: 15630 3.94 - 4.54: 21328 4.54 - 5.14: 32150 Nonbonded interactions: 79920 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH2 ARG A 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 296 " model vdw 2.139 3.120 nonbonded pdb=" O PHE D 257 " pdb=" OG SER D 260 " model vdw 2.343 3.040 ... (remaining 79915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.560 Find NCS groups from input model: 0.310 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8188 Z= 0.280 Angle : 0.581 4.978 11124 Z= 0.349 Chirality : 0.042 0.137 1320 Planarity : 0.006 0.049 1360 Dihedral : 12.964 89.336 2840 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.27), residues: 1028 helix: 1.57 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 172 HIS 0.001 0.000 HIS D 306 PHE 0.010 0.001 PHE B 289 TYR 0.020 0.002 TYR D 188 ARG 0.004 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.849 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.1758 time to fit residues: 135.1360 Evaluate side-chains 96 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.166257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115279 restraints weight = 8539.875| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.90 r_work: 0.3239 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8188 Z= 0.258 Angle : 0.515 4.399 11124 Z= 0.289 Chirality : 0.042 0.131 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.878 16.428 1148 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 7.11 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.06 (0.27), residues: 1028 helix: 1.87 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.37 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 362 HIS 0.001 0.000 HIS D 306 PHE 0.013 0.001 PHE B 257 TYR 0.018 0.002 TYR C 188 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.854 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 1.1814 time to fit residues: 135.7983 Evaluate side-chains 112 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.168212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117310 restraints weight = 8617.713| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.92 r_work: 0.3267 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8188 Z= 0.190 Angle : 0.479 4.514 11124 Z= 0.265 Chirality : 0.040 0.122 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.659 14.715 1148 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 8.77 % Favored : 90.28 % 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: 2.51 (0.28), residues: 1028 helix: 2.15 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.03 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS D 306 PHE 0.011 0.001 PHE A 257 TYR 0.018 0.002 TYR D 188 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.979 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 111 average time/residue: 1.1572 time to fit residues: 136.7158 Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.165992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115413 restraints weight = 8651.607| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.87 r_work: 0.3211 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8188 Z= 0.255 Angle : 0.501 4.494 11124 Z= 0.278 Chirality : 0.041 0.127 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.737 15.170 1148 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 9.95 % Favored : 88.63 % 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: 2.41 (0.28), residues: 1028 helix: 2.08 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.15 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 362 HIS 0.001 0.000 HIS A 179 PHE 0.011 0.001 PHE C 257 TYR 0.018 0.002 TYR D 188 ARG 0.002 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.859 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 1.2344 time to fit residues: 136.5038 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 86 optimal weight: 0.0060 chunk 48 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.169337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119446 restraints weight = 8613.828| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.86 r_work: 0.3256 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8188 Z= 0.158 Angle : 0.457 4.527 11124 Z= 0.253 Chirality : 0.039 0.117 1320 Planarity : 0.005 0.050 1360 Dihedral : 3.521 13.542 1148 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 10.90 % Favored : 87.68 % 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: 2.69 (0.28), residues: 1028 helix: 2.27 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.01 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 172 HIS 0.001 0.000 HIS C 306 PHE 0.009 0.001 PHE C 257 TYR 0.016 0.001 TYR A 188 ARG 0.001 0.000 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.878 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 1.1238 time to fit residues: 124.8671 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 49 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.170218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119698 restraints weight = 8573.489| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.91 r_work: 0.3290 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8188 Z= 0.163 Angle : 0.459 4.632 11124 Z= 0.252 Chirality : 0.039 0.116 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.409 12.815 1148 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.95 % Allowed : 12.80 % Favored : 86.26 % 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: 2.77 (0.28), residues: 1028 helix: 2.36 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.09 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 362 HIS 0.001 0.000 HIS D 179 PHE 0.009 0.001 PHE B 257 TYR 0.016 0.001 TYR B 188 ARG 0.001 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.839 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 96 average time/residue: 1.1655 time to fit residues: 119.2383 Evaluate side-chains 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117432 restraints weight = 8611.337| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.88 r_work: 0.3259 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8188 Z= 0.213 Angle : 0.486 4.728 11124 Z= 0.266 Chirality : 0.040 0.122 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.529 13.220 1148 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.07 % Allowed : 12.80 % 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: 2.69 (0.28), residues: 1028 helix: 2.28 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.04 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE B 257 TYR 0.015 0.002 TYR B 188 ARG 0.001 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.770 Fit side-chains REVERT: B 279 MET cc_start: 0.4978 (mtm) cc_final: 0.4454 (ptm) REVERT: C 279 MET cc_start: 0.4991 (mtm) cc_final: 0.4464 (ptm) REVERT: D 279 MET cc_start: 0.4977 (mtm) cc_final: 0.4454 (ptm) outliers start: 9 outliers final: 8 residues processed: 100 average time/residue: 1.1564 time to fit residues: 123.3110 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117476 restraints weight = 8677.198| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.89 r_work: 0.3236 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8188 Z= 0.220 Angle : 0.492 4.735 11124 Z= 0.269 Chirality : 0.040 0.122 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.553 13.443 1148 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.30 % Allowed : 12.44 % Favored : 86.26 % 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: 2.63 (0.28), residues: 1028 helix: 2.24 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.05 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 362 HIS 0.001 0.000 HIS B 179 PHE 0.009 0.001 PHE C 257 TYR 0.014 0.001 TYR A 188 ARG 0.001 0.000 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.795 Fit side-chains REVERT: A 279 MET cc_start: 0.5070 (mtm) cc_final: 0.4522 (ptm) REVERT: B 279 MET cc_start: 0.5058 (mtm) cc_final: 0.4527 (ptm) REVERT: C 279 MET cc_start: 0.5054 (mtm) cc_final: 0.4528 (ptm) REVERT: D 279 MET cc_start: 0.5062 (mtm) cc_final: 0.4532 (ptm) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 1.1774 time to fit residues: 126.6981 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 42 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.169925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120213 restraints weight = 8835.494| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.90 r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.161 Angle : 0.465 4.849 11124 Z= 0.254 Chirality : 0.039 0.115 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.398 12.311 1148 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.95 % Allowed : 12.91 % 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: 2.76 (0.28), residues: 1028 helix: 2.37 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.11 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 172 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE C 257 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.856 Fit side-chains REVERT: A 279 MET cc_start: 0.5227 (mtm) cc_final: 0.4787 (ptm) REVERT: B 279 MET cc_start: 0.5313 (mtm) cc_final: 0.4812 (ptm) REVERT: C 279 MET cc_start: 0.5306 (mtm) cc_final: 0.4805 (ptm) REVERT: D 279 MET cc_start: 0.5302 (mtm) cc_final: 0.4805 (ptm) outliers start: 8 outliers final: 8 residues processed: 109 average time/residue: 1.1898 time to fit residues: 138.3934 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.166941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117128 restraints weight = 8636.853| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.88 r_work: 0.3253 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8188 Z= 0.246 Angle : 0.515 5.327 11124 Z= 0.282 Chirality : 0.041 0.133 1320 Planarity : 0.005 0.050 1360 Dihedral : 3.575 13.604 1148 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.07 % Allowed : 12.68 % Favored : 86.26 % 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: 2.60 (0.28), residues: 1028 helix: 2.20 (0.19), residues: 804 sheet: None (None), residues: 0 loop : 0.01 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 362 HIS 0.001 0.000 HIS C 179 PHE 0.010 0.001 PHE C 257 TYR 0.014 0.002 TYR D 188 ARG 0.001 0.000 ARG B 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.912 Fit side-chains REVERT: A 279 MET cc_start: 0.5227 (mtm) cc_final: 0.4748 (ptm) REVERT: B 279 MET cc_start: 0.5230 (mtm) cc_final: 0.4762 (ptm) REVERT: C 279 MET cc_start: 0.5255 (mtm) cc_final: 0.4780 (ptm) REVERT: D 279 MET cc_start: 0.5238 (mtm) cc_final: 0.4769 (ptm) outliers start: 9 outliers final: 8 residues processed: 102 average time/residue: 1.1785 time to fit residues: 128.1572 Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.2082 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.171045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121899 restraints weight = 8769.287| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.92 r_work: 0.3330 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8188 Z= 0.142 Angle : 0.463 5.047 11124 Z= 0.253 Chirality : 0.038 0.112 1320 Planarity : 0.005 0.054 1360 Dihedral : 3.347 11.967 1148 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 13.27 % Favored : 85.78 % 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: 2.78 (0.28), residues: 1028 helix: 2.38 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.10 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 172 HIS 0.001 0.000 HIS D 306 PHE 0.008 0.001 PHE C 257 TYR 0.011 0.001 TYR B 188 ARG 0.001 0.000 ARG D 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6143.62 seconds wall clock time: 109 minutes 23.34 seconds (6563.34 seconds total)