Starting phenix.real_space_refine on Wed Mar 12 14:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uk5_26575/03_2025/7uk5_26575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uk5_26575/03_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_26575/03_2025/7uk5_26575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uk5_26575/03_2025/7uk5_26575.map" model { file = "/net/cci-nas-00/data/ceres_data/7uk5_26575/03_2025/7uk5_26575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uk5_26575/03_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-5624/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: 4.82, per 1000 atoms: 0.60 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 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: 0.72 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: 2.18 Time building geometry restraints manager: 2.55 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.350 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- 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 : 0.838 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.1511 time to fit residues: 132.6270 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 : 0.866 ------------------------------------------------------------------------------- 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 = 0.115278 restraints weight = 8539.875| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.90 r_work: 0.3238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.850 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 1.1553 time to fit residues: 133.3524 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 : 0.952 ------------------------------------------------------------------------------- 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: 0.8980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.167181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116009 restraints weight = 8604.989| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.92 r_work: 0.3249 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8188 Z= 0.223 Angle : 0.494 4.518 11124 Z= 0.274 Chirality : 0.041 0.126 1320 Planarity : 0.005 0.048 1360 Dihedral : 3.742 15.322 1148 Min Nonbonded Distance : 2.566 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: 2.41 (0.27), residues: 1028 helix: 2.08 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.05 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.001 0.000 HIS D 306 PHE 0.012 0.001 PHE A 257 TYR 0.018 0.002 TYR D 188 ARG 0.002 0.000 ARG D 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 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.848 Fit side-chains REVERT: A 347 LYS cc_start: 0.8240 (ptmt) cc_final: 0.8006 (ptmm) REVERT: B 347 LYS cc_start: 0.8241 (ptmt) cc_final: 0.8009 (ptmm) REVERT: C 347 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7990 (ptmm) REVERT: D 347 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7995 (ptmm) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 1.1165 time to fit residues: 119.2187 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 : 0.898 ------------------------------------------------------------------------------- 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: 0.6980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.169705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119703 restraints weight = 8676.142| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.88 r_work: 0.3290 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8188 Z= 0.154 Angle : 0.452 4.490 11124 Z= 0.250 Chirality : 0.039 0.117 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.502 13.484 1148 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.95 % Allowed : 9.48 % Favored : 89.57 % 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: 2.74 (0.28), residues: 1028 helix: 2.30 (0.19), residues: 800 sheet: None (None), residues: 0 loop : 0.09 (0.49), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 362 HIS 0.001 0.000 HIS D 306 PHE 0.010 0.001 PHE C 257 TYR 0.017 0.001 TYR A 188 ARG 0.001 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 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.861 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 115 average time/residue: 1.0807 time to fit residues: 132.9303 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.167715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117206 restraints weight = 8605.405| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.88 r_work: 0.3257 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8188 Z= 0.207 Angle : 0.473 4.642 11124 Z= 0.262 Chirality : 0.040 0.123 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.545 13.544 1148 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 11.85 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.28), residues: 1028 helix: 2.26 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.06 (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 A 179 PHE 0.010 0.001 PHE C 257 TYR 0.017 0.002 TYR B 188 ARG 0.001 0.000 ARG C 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 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.911 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 100 average time/residue: 1.0756 time to fit residues: 114.9594 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE 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: 0.0010 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.165395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114769 restraints weight = 8609.251| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.88 r_work: 0.3229 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8188 Z= 0.294 Angle : 0.528 4.711 11124 Z= 0.289 Chirality : 0.042 0.131 1320 Planarity : 0.005 0.047 1360 Dihedral : 3.778 15.201 1148 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.42 % Allowed : 12.68 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (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 0.007 0.002 TRP C 172 HIS 0.001 0.000 HIS A 179 PHE 0.011 0.001 PHE C 257 TYR 0.017 0.002 TYR B 188 ARG 0.001 0.000 ARG C 247 *********************** 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 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.962 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 103 average time/residue: 1.1061 time to fit residues: 122.0082 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE 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: 3.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116637 restraints weight = 8623.195| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.87 r_work: 0.3235 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1270 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= 0.232 Angle : 0.496 4.711 11124 Z= 0.274 Chirality : 0.040 0.124 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.677 14.729 1148 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 11.97 % Favored : 87.09 % 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: 2.47 (0.28), residues: 1028 helix: 2.11 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 172 HIS 0.001 0.000 HIS C 179 PHE 0.010 0.001 PHE A 257 TYR 0.015 0.002 TYR B 188 ARG 0.001 0.000 ARG D 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 97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.889 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 93 average time/residue: 1.1167 time to fit residues: 111.2997 Evaluate side-chains 97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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: 0.2980 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.167655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117706 restraints weight = 8688.304| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.88 r_work: 0.3264 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.199 Angle : 0.480 4.704 11124 Z= 0.265 Chirality : 0.040 0.120 1320 Planarity : 0.005 0.050 1360 Dihedral : 3.578 14.101 1148 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.07 % Allowed : 12.20 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.28), residues: 1028 helix: 2.16 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.08 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 172 HIS 0.001 0.000 HIS C 179 PHE 0.009 0.001 PHE B 257 TYR 0.014 0.001 TYR B 188 ARG 0.001 0.000 ARG C 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 102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.888 Fit side-chains REVERT: A 279 MET cc_start: 0.5206 (mtm) cc_final: 0.4656 (ptm) REVERT: B 279 MET cc_start: 0.5193 (mtm) cc_final: 0.4652 (ptm) REVERT: C 279 MET cc_start: 0.5179 (mtm) cc_final: 0.4637 (ptm) REVERT: D 279 MET cc_start: 0.5187 (mtm) cc_final: 0.4649 (ptm) outliers start: 9 outliers final: 9 residues processed: 98 average time/residue: 1.2212 time to fit residues: 127.7804 Evaluate side-chains 97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 290 VAL 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: 0.0000 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.4142 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.169506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119903 restraints weight = 8823.897| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.89 r_work: 0.3288 rms_B_bonded: 2.39 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: 0.7860 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8188 Z= 0.161 Angle : 0.469 4.774 11124 Z= 0.257 Chirality : 0.039 0.115 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.433 12.830 1148 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.07 % Allowed : 13.15 % 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: 2.66 (0.28), residues: 1028 helix: 2.28 (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 0.004 0.001 TRP D 172 HIS 0.001 0.000 HIS A 179 PHE 0.009 0.001 PHE D 257 TYR 0.012 0.001 TYR B 188 ARG 0.001 0.000 ARG C 296 *********************** 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 112 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.073 Fit side-chains REVERT: A 279 MET cc_start: 0.5330 (mtm) cc_final: 0.4834 (ptm) REVERT: B 279 MET cc_start: 0.5254 (mtm) cc_final: 0.4812 (ptm) REVERT: C 279 MET cc_start: 0.5247 (mtm) cc_final: 0.4804 (ptm) REVERT: D 279 MET cc_start: 0.5202 (mtm) cc_final: 0.4775 (ptm) outliers start: 9 outliers final: 9 residues processed: 108 average time/residue: 1.3534 time to fit residues: 155.8108 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 : 1.208 ------------------------------------------------------------------------------- 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 290 VAL 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: 0.6980 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.169033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119312 restraints weight = 8594.851| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.89 r_work: 0.3275 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.190 Angle : 0.488 5.345 11124 Z= 0.266 Chirality : 0.039 0.119 1320 Planarity : 0.005 0.053 1360 Dihedral : 3.463 13.228 1148 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.07 % Allowed : 13.63 % Favored : 85.31 % 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: 2.64 (0.28), residues: 1028 helix: 2.27 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.12 (0.48), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS C 179 PHE 0.009 0.001 PHE B 257 TYR 0.013 0.001 TYR D 188 ARG 0.001 0.000 ARG C 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 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.846 Fit side-chains REVERT: A 279 MET cc_start: 0.5221 (mtm) cc_final: 0.4761 (ptm) REVERT: B 279 MET cc_start: 0.5183 (mtm) cc_final: 0.4759 (ptm) REVERT: C 279 MET cc_start: 0.5177 (mtm) cc_final: 0.4753 (ptm) REVERT: D 279 MET cc_start: 0.5165 (mtm) cc_final: 0.4749 (ptm) outliers start: 9 outliers final: 9 residues processed: 97 average time/residue: 1.1415 time to fit residues: 117.9413 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 290 VAL 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: 0.7980 chunk 61 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.0070 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120226 restraints weight = 8685.998| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.90 r_work: 0.3292 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.173 Angle : 0.481 5.383 11124 Z= 0.262 Chirality : 0.039 0.117 1320 Planarity : 0.005 0.054 1360 Dihedral : 3.409 12.899 1148 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.07 % Allowed : 13.15 % 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: 2.68 (0.28), residues: 1028 helix: 2.30 (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 0.004 0.001 TRP D 172 HIS 0.001 0.000 HIS D 179 PHE 0.009 0.001 PHE D 257 TYR 0.013 0.001 TYR B 188 ARG 0.001 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6035.82 seconds wall clock time: 104 minutes 23.13 seconds (6263.13 seconds total)