Starting phenix.real_space_refine on Mon Feb 10 22:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkh_14042/02_2025/7qkh_14042.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 S 6 5.16 5 C 945 2.51 5 N 273 2.21 5 O 288 1.98 5 H 1593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "B" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "D" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 523 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 512 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 1.92, per 1000 atoms: 0.62 Number of scatterers: 3105 At special positions: 0 Unit cell: (58.16, 139.584, 33.442, 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) S 6 16.00 O 288 8.00 N 273 7.00 C 945 6.00 H 1593 1.00 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: 0.75 Conformation dependent library (CDL) restraints added in 210.2 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA2, first strand: chain 'B' and resid 279 through 282 Processing sheet with id=AA3, first strand: chain 'B' and resid 296 through 297 removed outlier: 6.313A pdb=" N ASN A 296 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 305 through 309 removed outlier: 6.260A pdb=" N VAL A 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL D 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.460A pdb=" N LYS G 294 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 298 through 299 removed outlier: 6.582A pdb=" N LYS G 298 " --> pdb=" O HIS E 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.383A pdb=" N VAL G 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 316 32 hydrogen bonds defined for protein. 96 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: 0.90 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 1586 1.09 - 1.27: 256 1.27 - 1.45: 348 1.45 - 1.63: 924 1.63 - 1.81: 6 Bond restraints: 3120 Sorted by residual: bond pdb=" N ILE A 297 " pdb=" H ILE A 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE G 297 " pdb=" H ILE G 297 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS B 298 " pdb=" H LYS B 298 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N HIS D 299 " pdb=" H HIS D 299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" NE2 GLN B 307 " pdb="HE21 GLN B 307 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.40: 5614 7.40 - 14.80: 48 14.80 - 22.21: 7 22.21 - 29.61: 9 29.61 - 37.01: 13 Bond angle restraints: 5691 Sorted by residual: angle pdb=" CB VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 109.00 71.99 37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA VAL E 313 " pdb=" CB VAL E 313 " pdb=" HB VAL E 313 " ideal model delta sigma weight residual 109.00 72.93 36.07 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" HA VAL G 313 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N VAL E 313 " pdb=" CA VAL E 313 " pdb=" HA VAL E 313 " ideal model delta sigma weight residual 110.00 74.59 35.41 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" HA VAL C 313 " ideal model delta sigma weight residual 110.00 75.23 34.77 3.00e+00 1.11e-01 1.34e+02 ... (remaining 5686 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.34: 1193 15.34 - 30.66: 151 30.66 - 45.99: 31 45.99 - 61.32: 43 61.32 - 76.65: 25 Dihedral angle restraints: 1443 sinusoidal: 837 harmonic: 606 Sorted by residual: dihedral pdb=" C VAL C 313 " pdb=" N VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual -122.00 -141.49 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" C VAL G 313 " pdb=" N VAL G 313 " pdb=" CA VAL G 313 " pdb=" CB VAL G 313 " ideal model delta harmonic sigma weight residual -122.00 -139.63 17.63 0 2.50e+00 1.60e-01 4.97e+01 dihedral pdb=" N VAL C 313 " pdb=" C VAL C 313 " pdb=" CA VAL C 313 " pdb=" CB VAL C 313 " ideal model delta harmonic sigma weight residual 123.40 140.78 -17.38 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 222 0.248 - 0.495: 8 0.495 - 0.743: 3 0.743 - 0.990: 3 0.990 - 1.238: 1 Chirality restraints: 237 Sorted by residual: chirality pdb=" CB VAL G 313 " pdb=" CA VAL G 313 " pdb=" CG1 VAL G 313 " pdb=" CG2 VAL G 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL G 287 " pdb=" CA VAL G 287 " pdb=" CG1 VAL G 287 " pdb=" CG2 VAL G 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.65 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CB VAL C 287 " pdb=" CA VAL C 287 " pdb=" CG1 VAL C 287 " pdb=" CG2 VAL C 287 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 234 not shown) Planarity restraints: 447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 286 " -0.024 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG ASN B 286 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 286 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN B 286 " 0.171 2.00e-02 2.50e+03 pdb="HD21 ASN B 286 " -0.080 2.00e-02 2.50e+03 pdb="HD22 ASN B 286 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.116 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 286 " -0.043 2.00e-02 2.50e+03 6.96e-02 7.27e+01 pdb=" CG ASN A 286 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 286 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 286 " 0.134 2.00e-02 2.50e+03 pdb="HD21 ASN A 286 " -0.020 2.00e-02 2.50e+03 pdb="HD22 ASN A 286 " -0.093 2.00e-02 2.50e+03 ... (remaining 444 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 396 2.26 - 2.84: 6035 2.84 - 3.43: 8037 3.43 - 4.01: 10197 4.01 - 4.60: 14619 Nonbonded interactions: 39284 Sorted by model distance: nonbonded pdb=" H VAL C 313 " pdb=" HA VAL C 313 " model vdw 1.669 1.816 nonbonded pdb=" HZ3 LYS G 294 " pdb=" OD2 ASP B 295 " model vdw 1.697 2.450 nonbonded pdb=" H VAL E 313 " pdb=" HA VAL E 313 " model vdw 1.701 1.816 nonbonded pdb="HG21 ILE B 277 " pdb=" H ILE B 278 " model vdw 1.719 2.270 nonbonded pdb=" H VAL G 313 " pdb=" HA VAL G 313 " model vdw 1.720 1.816 ... (remaining 39279 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } 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: 0.320 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: 0.060 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.011 0.039 1527 Z= 0.743 Angle : 2.478 18.649 2043 Z= 1.587 Chirality : 0.194 1.238 237 Planarity : 0.012 0.062 258 Dihedral : 15.219 74.648 585 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Cbeta Deviations : 2.78 % 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: -3.56 (0.42), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.32), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 299 TYR 0.109 0.031 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: C 290 LYS cc_start: 0.7765 (pttt) cc_final: 0.5962 (mmtm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.4269 time to fit residues: 14.4481 Evaluate side-chains 18 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.131216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.119840 restraints weight = 7369.154| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.23 r_work: 0.4283 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1527 Z= 0.271 Angle : 1.078 11.772 2043 Z= 0.567 Chirality : 0.218 1.496 237 Planarity : 0.003 0.020 258 Dihedral : 9.055 24.027 204 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.56 % Allowed : 16.67 % Favored : 82.78 % 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: -3.21 (0.43), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 299 TYR 0.014 0.003 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.276 Fit side-chains REVERT: G 305 SER cc_start: 0.8306 (p) cc_final: 0.7895 (m) REVERT: C 290 LYS cc_start: 0.8022 (pttt) cc_final: 0.5410 (mmtm) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.2671 time to fit residues: 6.3093 Evaluate side-chains 17 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.129813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.118294 restraints weight = 7586.330| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.20 r_work: 0.4255 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1527 Z= 0.241 Angle : 1.010 11.235 2043 Z= 0.534 Chirality : 0.219 1.479 237 Planarity : 0.004 0.026 258 Dihedral : 8.316 21.061 204 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 299 TYR 0.014 0.003 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: C 290 LYS cc_start: 0.8044 (pttt) cc_final: 0.5335 (mmtm) REVERT: E 305 SER cc_start: 0.8295 (p) cc_final: 0.7839 (m) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.3030 time to fit residues: 7.3708 Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.121930 restraints weight = 7335.768| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.31 r_work: 0.4290 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1527 Z= 0.206 Angle : 0.935 11.060 2043 Z= 0.493 Chirality : 0.217 1.464 237 Planarity : 0.004 0.031 258 Dihedral : 7.055 19.660 204 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.015 0.002 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: G 290 LYS cc_start: 0.7761 (pttt) cc_final: 0.7434 (ptpp) REVERT: B 290 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7219 (tptt) REVERT: B 308 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7197 (mt) REVERT: D 309 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8075 (p) REVERT: E 305 SER cc_start: 0.8142 (p) cc_final: 0.7903 (m) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.2466 time to fit residues: 5.8315 Evaluate side-chains 22 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.135277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.123469 restraints weight = 7348.310| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.29 r_work: 0.4311 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4231 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1527 Z= 0.193 Angle : 0.917 11.250 2043 Z= 0.482 Chirality : 0.219 1.485 237 Planarity : 0.004 0.036 258 Dihedral : 6.524 18.904 204 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.22 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 TYR 0.013 0.002 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.253 Fit side-chains REVERT: B 290 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7237 (tptt) REVERT: B 308 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7141 (mt) REVERT: E 310 TYR cc_start: 0.8138 (t80) cc_final: 0.7458 (t80) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.2463 time to fit residues: 6.4197 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.125568 restraints weight = 7362.226| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.32 r_work: 0.4323 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4243 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.191 Angle : 0.903 11.109 2043 Z= 0.475 Chirality : 0.218 1.471 237 Planarity : 0.004 0.037 258 Dihedral : 6.111 18.309 204 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 18.33 % Favored : 80.56 % 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 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.015 0.002 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.278 Fit side-chains REVERT: B 290 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7241 (tptt) REVERT: E 310 TYR cc_start: 0.8276 (t80) cc_final: 0.7631 (t80) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.2671 time to fit residues: 5.1605 Evaluate side-chains 18 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.120254 restraints weight = 7524.436| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.36 r_work: 0.4265 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1527 Z= 0.222 Angle : 0.921 11.299 2043 Z= 0.483 Chirality : 0.219 1.492 237 Planarity : 0.004 0.036 258 Dihedral : 6.404 17.647 204 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.22 % Allowed : 17.78 % Favored : 80.00 % 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: -3.01 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 299 TYR 0.010 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: B 308 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7222 (mt) REVERT: C 284 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6897 (mp) REVERT: D 309 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8169 (p) outliers start: 4 outliers final: 1 residues processed: 17 average time/residue: 0.2669 time to fit residues: 5.4607 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.136429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.124493 restraints weight = 7221.499| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 2.26 r_work: 0.4318 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1527 Z= 0.185 Angle : 0.890 11.026 2043 Z= 0.468 Chirality : 0.217 1.466 237 Planarity : 0.004 0.035 258 Dihedral : 5.824 17.311 204 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 18.33 % Favored : 80.56 % 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: -2.85 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.010 0.001 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: B 308 ILE cc_start: 0.7447 (tt) cc_final: 0.7140 (mt) REVERT: C 284 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6849 (mp) REVERT: E 310 TYR cc_start: 0.8333 (t80) cc_final: 0.7768 (t80) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.2310 time to fit residues: 5.0627 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.139737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.127785 restraints weight = 7261.293| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.28 r_work: 0.4368 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4288 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.189 Angle : 0.884 11.171 2043 Z= 0.463 Chirality : 0.218 1.475 237 Planarity : 0.004 0.034 258 Dihedral : 5.395 16.420 204 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.11 % Allowed : 18.33 % Favored : 80.56 % 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 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.008 0.001 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 290 LYS cc_start: 0.7720 (pttt) cc_final: 0.7315 (ptpp) REVERT: B 308 ILE cc_start: 0.7467 (tt) cc_final: 0.7120 (mt) REVERT: C 284 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7192 (mp) REVERT: E 310 TYR cc_start: 0.8275 (t80) cc_final: 0.7728 (t80) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.2999 time to fit residues: 7.2292 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.138804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.126729 restraints weight = 7096.051| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.30 r_work: 0.4350 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4269 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.190 Angle : 0.889 11.156 2043 Z= 0.465 Chirality : 0.218 1.473 237 Planarity : 0.004 0.034 258 Dihedral : 5.396 16.247 204 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.56 % Allowed : 18.89 % Favored : 80.56 % 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: -2.75 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.007 0.001 TYR E 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 290 LYS cc_start: 0.7772 (pttt) cc_final: 0.7359 (ptpp) REVERT: B 308 ILE cc_start: 0.7577 (tt) cc_final: 0.7174 (mt) REVERT: C 284 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7235 (mp) REVERT: E 310 TYR cc_start: 0.8262 (t80) cc_final: 0.7711 (t80) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.3115 time to fit residues: 6.8972 Evaluate side-chains 20 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.139930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.127677 restraints weight = 7180.135| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.33 r_work: 0.4379 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4298 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1527 Z= 0.190 Angle : 0.883 11.130 2043 Z= 0.463 Chirality : 0.218 1.471 237 Planarity : 0.004 0.035 258 Dihedral : 5.271 16.085 204 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.56 % Allowed : 18.33 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.007 0.001 TYR E 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.67 seconds wall clock time: 45 minutes 47.86 seconds (2747.86 seconds total)