Starting phenix.real_space_refine on Wed Jun 4 09:58:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkz_14058/06_2025/7qkz_14058.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 540 2.51 5 N 126 2.21 5 O 144 1.98 5 H 891 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 1701 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "F" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "H" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "I" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Time building chain proxies: 1.05, per 1000 atoms: 0.62 Number of scatterers: 1701 At special positions: 0 Unit cell: (58.464, 57.456, 29.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 144 8.00 N 126 7.00 C 540 6.00 H 891 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: 0.40 Conformation dependent library (CDL) restraints added in 399.9 milliseconds 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 198 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.096A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.645A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.053A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.544A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.115A pdb=" N ILE G 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.554A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) 9 hydrogen bonds defined for protein. 27 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: 0.42 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.08: 215 1.08 - 1.20: 676 1.20 - 1.33: 197 1.33 - 1.46: 147 1.46 - 1.59: 475 Bond restraints: 1710 Sorted by residual: bond pdb=" N LYS A 311 " pdb=" H LYS A 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N SER D 316 " pdb=" H SER D 316 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CD1 TYR E 310 " pdb=" HD1 TYR E 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CE1 TYR D 310 " pdb=" HE1 TYR D 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 1705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.85: 3065 7.85 - 15.69: 13 15.69 - 23.54: 14 23.54 - 31.39: 32 31.39 - 39.23: 17 Bond angle restraints: 3141 Sorted by residual: angle pdb=" CA VAL H 313 " pdb=" CB VAL H 313 " pdb=" CG1 VAL H 313 " ideal model delta sigma weight residual 110.40 135.78 -25.38 1.70e+00 3.46e-01 2.23e+02 angle pdb=" CA VAL E 313 " pdb=" CB VAL E 313 " pdb=" CG1 VAL E 313 " ideal model delta sigma weight residual 110.40 133.04 -22.64 1.70e+00 3.46e-01 1.77e+02 angle pdb=" N VAL I 309 " pdb=" CA VAL I 309 " pdb=" HA VAL I 309 " ideal model delta sigma weight residual 110.00 70.77 39.23 3.00e+00 1.11e-01 1.71e+02 angle pdb=" N VAL D 309 " pdb=" CA VAL D 309 " pdb=" HA VAL D 309 " ideal model delta sigma weight residual 110.00 71.91 38.09 3.00e+00 1.11e-01 1.61e+02 angle pdb=" N VAL H 309 " pdb=" CA VAL H 309 " pdb=" HA VAL H 309 " ideal model delta sigma weight residual 110.00 72.16 37.84 3.00e+00 1.11e-01 1.59e+02 ... (remaining 3136 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.69: 703 17.69 - 35.37: 57 35.37 - 53.05: 9 53.05 - 70.73: 13 70.73 - 88.41: 10 Dihedral angle restraints: 792 sinusoidal: 459 harmonic: 333 Sorted by residual: dihedral pdb=" C VAL E 309 " pdb=" N VAL E 309 " pdb=" CA VAL E 309 " pdb=" CB VAL E 309 " ideal model delta harmonic sigma weight residual -122.00 -143.28 21.28 0 2.50e+00 1.60e-01 7.25e+01 dihedral pdb=" C VAL F 309 " pdb=" N VAL F 309 " pdb=" CA VAL F 309 " pdb=" CB VAL F 309 " ideal model delta harmonic sigma weight residual -122.00 -142.70 20.70 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" C VAL C 309 " pdb=" N VAL C 309 " pdb=" CA VAL C 309 " pdb=" CB VAL C 309 " ideal model delta harmonic sigma weight residual -122.00 -142.58 20.58 0 2.50e+00 1.60e-01 6.77e+01 ... (remaining 789 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.234: 104 0.234 - 0.467: 16 0.467 - 0.700: 2 0.700 - 0.934: 5 0.934 - 1.167: 8 Chirality restraints: 135 Sorted by residual: chirality pdb=" CB VAL F 313 " pdb=" CA VAL F 313 " pdb=" CG1 VAL F 313 " pdb=" CG2 VAL F 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.46 -1.17 2.00e-01 2.50e+01 3.40e+01 chirality pdb=" CB VAL D 313 " pdb=" CA VAL D 313 " pdb=" CG1 VAL D 313 " pdb=" CG2 VAL D 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.48 -1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CB VAL H 313 " pdb=" CA VAL H 313 " pdb=" CG1 VAL H 313 " pdb=" CG2 VAL H 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 132 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.180 2.00e-02 2.50e+03 7.10e-02 1.51e+02 pdb=" CG TYR G 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 TYR G 310 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR G 310 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR G 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR G 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " 0.168 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR H 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " 0.115 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.161 2.00e-02 2.50e+03 6.48e-02 1.26e+02 pdb=" CG TYR A 310 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.015 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.13: 193 2.13 - 2.72: 2366 2.72 - 3.32: 4863 3.32 - 3.91: 5809 3.91 - 4.50: 7975 Nonbonded interactions: 21206 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.546 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.547 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.548 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.550 2.450 ... (remaining 21201 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.700 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.080 Find NCS groups from input model: 0.050 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:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 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 : 0.013 0.049 819 Z= 0.720 Angle : 2.863 25.384 1098 Z= 1.799 Chirality : 0.342 1.167 135 Planarity : 0.023 0.081 126 Dihedral : 18.752 88.410 324 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 9.09 % 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: -1.61 (0.95), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.154 0.052 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.07870 ( 9) hydrogen bonds : angle 10.26161 ( 27) covalent geometry : bond 0.01287 ( 819) covalent geometry : angle 2.86324 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.155 Fit side-chains REVERT: B 307 GLN cc_start: 0.5904 (mp-120) cc_final: 0.4972 (pp30) REVERT: A 308 ILE cc_start: 0.8090 (mm) cc_final: 0.7853 (mm) REVERT: C 307 GLN cc_start: 0.5932 (mp-120) cc_final: 0.5356 (pp30) REVERT: D 307 GLN cc_start: 0.6185 (mp-120) cc_final: 0.5207 (pp30) REVERT: E 307 GLN cc_start: 0.6420 (mp-120) cc_final: 0.5476 (pp30) REVERT: F 307 GLN cc_start: 0.6410 (mp-120) cc_final: 0.5451 (pp30) REVERT: G 307 GLN cc_start: 0.5394 (mp-120) cc_final: 0.4893 (pp30) REVERT: I 307 GLN cc_start: 0.6387 (mp-120) cc_final: 0.5461 (pp30) outliers start: 0 outliers final: 1 residues processed: 41 average time/residue: 2.2941 time to fit residues: 94.9122 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 308 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.251246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.243692 restraints weight = 2885.910| |-----------------------------------------------------------------------------| r_work (start): 0.5260 rms_B_bonded: 1.70 r_work: 0.5209 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.5139 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.5139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 819 Z= 0.210 Angle : 1.537 10.964 1098 Z= 0.828 Chirality : 0.373 1.446 135 Planarity : 0.008 0.038 126 Dihedral : 7.744 18.817 101 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.01 % Allowed : 26.26 % Favored : 72.73 % 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: -1.88 (0.90), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.004 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.02691 ( 9) hydrogen bonds : angle 8.42717 ( 27) covalent geometry : bond 0.00597 ( 819) covalent geometry : angle 1.53696 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 307 GLN cc_start: 0.6145 (mp-120) cc_final: 0.5288 (tm-30) REVERT: A 307 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5242 (pp30) REVERT: C 307 GLN cc_start: 0.5728 (mp-120) cc_final: 0.5478 (pt0) REVERT: D 307 GLN cc_start: 0.6277 (mp-120) cc_final: 0.5519 (pt0) REVERT: E 307 GLN cc_start: 0.6031 (mp-120) cc_final: 0.5716 (pp30) REVERT: F 307 GLN cc_start: 0.6045 (mp-120) cc_final: 0.5317 (pt0) REVERT: I 307 GLN cc_start: 0.6010 (mp-120) cc_final: 0.5144 (pt0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 1.9689 time to fit residues: 39.9706 Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9483 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN H 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.250714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.243091 restraints weight = 2898.120| |-----------------------------------------------------------------------------| r_work (start): 0.5251 rms_B_bonded: 1.71 r_work: 0.5205 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.5127 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.5127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.8192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.199 Angle : 1.516 10.989 1098 Z= 0.818 Chirality : 0.377 1.477 135 Planarity : 0.008 0.040 126 Dihedral : 6.775 14.705 99 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.03 % Allowed : 26.26 % Favored : 70.71 % 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: -1.91 (0.89), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR E 310 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 9) hydrogen bonds : angle 7.89486 ( 27) covalent geometry : bond 0.00600 ( 819) covalent geometry : angle 1.51638 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 GLN cc_start: 0.6468 (mp-120) cc_final: 0.5567 (tm-30) REVERT: A 307 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5343 (tm130) REVERT: D 307 GLN cc_start: 0.6303 (mp-120) cc_final: 0.5399 (tm-30) REVERT: E 307 GLN cc_start: 0.5990 (mp-120) cc_final: 0.5630 (pp30) REVERT: F 307 GLN cc_start: 0.6191 (mp-120) cc_final: 0.5391 (pt0) REVERT: I 317 LYS cc_start: 0.5359 (mtmt) cc_final: 0.4270 (mtmt) outliers start: 3 outliers final: 0 residues processed: 17 average time/residue: 2.3186 time to fit residues: 39.9107 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN H 307 GLN I 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.257601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.248806 restraints weight = 2784.390| |-----------------------------------------------------------------------------| r_work (start): 0.5236 rms_B_bonded: 1.83 r_work: 0.5190 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.5117 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.5117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.8583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.191 Angle : 1.493 10.959 1098 Z= 0.805 Chirality : 0.378 1.481 135 Planarity : 0.008 0.040 126 Dihedral : 6.388 16.034 99 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 27.27 % Favored : 69.70 % 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: -2.12 (0.88), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.67), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 9) hydrogen bonds : angle 7.74472 ( 27) covalent geometry : bond 0.00584 ( 819) covalent geometry : angle 1.49343 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5506 (tm130) REVERT: C 307 GLN cc_start: 0.5854 (mp10) cc_final: 0.5233 (tm-30) REVERT: D 307 GLN cc_start: 0.6230 (mp-120) cc_final: 0.5653 (tm-30) REVERT: I 317 LYS cc_start: 0.5294 (mtmt) cc_final: 0.3993 (tppt) outliers start: 3 outliers final: 0 residues processed: 17 average time/residue: 2.0741 time to fit residues: 35.9966 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 overall best weight: 0.6230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN F 307 GLN I 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5284 r_free = 0.5284 target = 0.257126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.249255 restraints weight = 2862.409| |-----------------------------------------------------------------------------| r_work (start): 0.5219 rms_B_bonded: 1.72 r_work: 0.5177 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.5112 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.5112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.188 Angle : 1.488 10.970 1098 Z= 0.801 Chirality : 0.378 1.476 135 Planarity : 0.007 0.038 126 Dihedral : 6.044 15.172 99 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 27.27 % Favored : 69.70 % 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: -1.99 (0.89), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.68), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02581 ( 9) hydrogen bonds : angle 7.62712 ( 27) covalent geometry : bond 0.00577 ( 819) covalent geometry : angle 1.48755 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 307 GLN cc_start: 0.6203 (mp10) cc_final: 0.5348 (tm-30) REVERT: A 307 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5287 (pp30) REVERT: C 317 LYS cc_start: 0.5531 (mtmt) cc_final: 0.4152 (tppt) REVERT: D 307 GLN cc_start: 0.6312 (mp-120) cc_final: 0.5777 (tm-30) REVERT: I 317 LYS cc_start: 0.5335 (mtmt) cc_final: 0.4064 (tppt) outliers start: 3 outliers final: 0 residues processed: 21 average time/residue: 1.6111 time to fit residues: 34.3973 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN F 307 GLN I 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.253989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.246482 restraints weight = 2896.938| |-----------------------------------------------------------------------------| r_work (start): 0.5220 rms_B_bonded: 1.71 r_work: 0.5185 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.5123 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.5123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.9242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.190 Angle : 1.485 10.993 1098 Z= 0.799 Chirality : 0.378 1.463 135 Planarity : 0.007 0.037 126 Dihedral : 5.966 15.682 99 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.03 % Allowed : 30.30 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.90), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 9) hydrogen bonds : angle 7.57735 ( 27) covalent geometry : bond 0.00577 ( 819) covalent geometry : angle 1.48546 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.4800 (pp30) REVERT: C 317 LYS cc_start: 0.5428 (mtmt) cc_final: 0.4046 (tppt) REVERT: I 317 LYS cc_start: 0.5307 (mtmt) cc_final: 0.3997 (tppt) outliers start: 3 outliers final: 0 residues processed: 18 average time/residue: 1.3737 time to fit residues: 25.2560 Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.254492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.246486 restraints weight = 2825.779| |-----------------------------------------------------------------------------| r_work (start): 0.5226 rms_B_bonded: 1.73 r_work: 0.5183 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.5109 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.5109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.9444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.189 Angle : 1.488 10.965 1098 Z= 0.799 Chirality : 0.378 1.453 135 Planarity : 0.007 0.037 126 Dihedral : 5.733 12.589 99 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 32.32 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.91), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 310 Details of bonding type rmsd hydrogen bonds : bond 0.02145 ( 9) hydrogen bonds : angle 7.47846 ( 27) covalent geometry : bond 0.00578 ( 819) covalent geometry : angle 1.48815 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.4827 (tm130) REVERT: C 317 LYS cc_start: 0.5423 (mtmt) cc_final: 0.3997 (tppt) REVERT: I 317 LYS cc_start: 0.5254 (mtmt) cc_final: 0.3928 (tppt) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 1.2066 time to fit residues: 22.2364 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain I residue 307 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.254706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.246442 restraints weight = 2803.879| |-----------------------------------------------------------------------------| r_work (start): 0.5226 rms_B_bonded: 1.74 r_work: 0.5190 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.5123 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.5123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.9536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 819 Z= 0.193 Angle : 1.486 10.962 1098 Z= 0.797 Chirality : 0.378 1.454 135 Planarity : 0.007 0.036 126 Dihedral : 5.630 12.025 99 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.02 % Allowed : 31.31 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.90), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.69), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 310 Details of bonding type rmsd hydrogen bonds : bond 0.02019 ( 9) hydrogen bonds : angle 7.47709 ( 27) covalent geometry : bond 0.00583 ( 819) covalent geometry : angle 1.48572 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.4868 (tm130) REVERT: C 317 LYS cc_start: 0.5471 (mtmt) cc_final: 0.4071 (tppt) REVERT: I 317 LYS cc_start: 0.5229 (mtmt) cc_final: 0.3906 (tppt) outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 1.3013 time to fit residues: 22.6336 Evaluate side-chains 16 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.254303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.246163 restraints weight = 2857.077| |-----------------------------------------------------------------------------| r_work (start): 0.5208 rms_B_bonded: 1.76 r_work: 0.5154 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.5079 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.9641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.194 Angle : 1.493 11.043 1098 Z= 0.803 Chirality : 0.377 1.459 135 Planarity : 0.007 0.036 126 Dihedral : 5.631 13.573 99 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 31.31 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.92), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.02137 ( 9) hydrogen bonds : angle 7.21808 ( 27) covalent geometry : bond 0.00585 ( 819) covalent geometry : angle 1.49271 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.4922 (tt0) REVERT: C 317 LYS cc_start: 0.5411 (mtmt) cc_final: 0.3995 (tppt) REVERT: F 317 LYS cc_start: 0.5490 (mtmt) cc_final: 0.4132 (tppt) REVERT: I 317 LYS cc_start: 0.5308 (mtmt) cc_final: 0.3914 (tppt) outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 1.5303 time to fit residues: 20.3199 Evaluate side-chains 11 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.253710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.245478 restraints weight = 2971.558| |-----------------------------------------------------------------------------| r_work (start): 0.5215 rms_B_bonded: 1.80 r_work: 0.5171 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.5103 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.5103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.9749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 819 Z= 0.191 Angle : 1.495 10.984 1098 Z= 0.804 Chirality : 0.377 1.461 135 Planarity : 0.007 0.035 126 Dihedral : 5.748 19.720 99 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.02 % Allowed : 32.32 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.91), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR E 310 Details of bonding type rmsd hydrogen bonds : bond 0.02196 ( 9) hydrogen bonds : angle 7.22177 ( 27) covalent geometry : bond 0.00577 ( 819) covalent geometry : angle 1.49455 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.7708 (t80) cc_final: 0.7348 (t80) REVERT: A 307 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.4926 (tt0) REVERT: C 317 LYS cc_start: 0.5351 (mtmt) cc_final: 0.3890 (tppt) REVERT: F 317 LYS cc_start: 0.5453 (mtmt) cc_final: 0.4050 (tppt) REVERT: I 317 LYS cc_start: 0.5334 (mtmt) cc_final: 0.3860 (tppt) outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 1.4529 time to fit residues: 20.7959 Evaluate side-chains 14 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.250307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5197 r_free = 0.5197 target = 0.242940 restraints weight = 2876.482| |-----------------------------------------------------------------------------| r_work (start): 0.5225 rms_B_bonded: 1.62 r_work: 0.5186 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.5117 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.5117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.9782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.192 Angle : 1.492 10.950 1098 Z= 0.803 Chirality : 0.377 1.460 135 Planarity : 0.007 0.035 126 Dihedral : 5.461 14.011 99 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 32.32 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.92), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.70), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 310 Details of bonding type rmsd hydrogen bonds : bond 0.01728 ( 9) hydrogen bonds : angle 7.11707 ( 27) covalent geometry : bond 0.00583 ( 819) covalent geometry : angle 1.49200 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2440.59 seconds wall clock time: 42 minutes 16.24 seconds (2536.24 seconds total)