Starting phenix.real_space_refine on Tue Mar 3 10:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vqq_32092/03_2026/7vqq_32092.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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: 3 Type Number sf(0) Gaussians C 1158 2.51 5 N 327 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1968 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "B" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "C" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Time building chain proxies: 0.91, per 1000 atoms: 0.46 Number of scatterers: 1968 At special positions: 0 Unit cell: (80.3, 83.6, 30.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 483 8.00 N 327 7.00 C 1158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 207.2 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 444 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 6.676A pdb=" N SER A 56 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 56 " --> pdb=" O SER C 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.353A pdb=" N ASN B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.503A pdb=" N SER C 70 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.734A pdb=" N GLN A 73 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN B 73 " --> pdb=" O GLY C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.345A pdb=" N TYR A 81 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 81 " --> pdb=" O GLY C 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 93 through 96 10 hydrogen bonds defined for protein. 30 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: 0.21 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 333 1.28 - 1.35: 322 1.35 - 1.41: 337 1.41 - 1.47: 346 1.47 - 1.54: 681 Bond restraints: 2019 Sorted by residual: bond pdb=" C ALA A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 5.02e+00 bond pdb=" C TYR B 91 " pdb=" N GLY B 92 " ideal model delta sigma weight residual 1.330 1.308 0.021 1.31e-02 5.83e+03 2.64e+00 bond pdb=" CA GLY B 92 " pdb=" C GLY B 92 " ideal model delta sigma weight residual 1.517 1.496 0.021 1.43e-02 4.89e+03 2.24e+00 bond pdb=" CA GLN C 118 " pdb=" CB GLN C 118 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.69e-02 3.50e+03 2.04e+00 bond pdb=" N GLY A 65 " pdb=" CA GLY A 65 " ideal model delta sigma weight residual 1.460 1.442 0.018 1.26e-02 6.30e+03 2.03e+00 ... (remaining 2014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2352 1.11 - 2.22: 306 2.22 - 3.33: 57 3.33 - 4.44: 14 4.44 - 5.55: 4 Bond angle restraints: 2733 Sorted by residual: angle pdb=" CA TYR C 38 " pdb=" CB TYR C 38 " pdb=" CG TYR C 38 " ideal model delta sigma weight residual 113.90 108.92 4.98 1.80e+00 3.09e-01 7.64e+00 angle pdb=" CA GLY C 82 " pdb=" C GLY C 82 " pdb=" N SER C 83 " ideal model delta sigma weight residual 115.49 118.02 -2.53 1.03e+00 9.43e-01 6.01e+00 angle pdb=" CA GLY C 76 " pdb=" C GLY C 76 " pdb=" N SER C 77 " ideal model delta sigma weight residual 115.09 118.18 -3.09 1.29e+00 6.01e-01 5.73e+00 angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 109.60 4.30 1.80e+00 3.09e-01 5.72e+00 angle pdb=" N GLY A 59 " pdb=" CA GLY A 59 " pdb=" C GLY A 59 " ideal model delta sigma weight residual 113.18 118.73 -5.55 2.37e+00 1.78e-01 5.49e+00 ... (remaining 2728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.17: 1007 13.17 - 26.34: 117 26.34 - 39.51: 19 39.51 - 52.68: 4 52.68 - 65.85: 2 Dihedral angle restraints: 1149 sinusoidal: 390 harmonic: 759 Sorted by residual: dihedral pdb=" CA TYR A 91 " pdb=" C TYR A 91 " pdb=" N GLY A 92 " pdb=" CA GLY A 92 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLY C 92 " pdb=" CA GLY C 92 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 58 " pdb=" C TYR B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 143 0.029 - 0.057: 52 0.057 - 0.086: 28 0.086 - 0.115: 13 0.115 - 0.143: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA TYR B 41 " pdb=" N TYR B 41 " pdb=" C TYR B 41 " pdb=" CB TYR B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA TYR C 41 " pdb=" N TYR C 41 " pdb=" C TYR C 41 " pdb=" CB TYR C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA TYR A 41 " pdb=" N TYR A 41 " pdb=" C TYR A 41 " pdb=" CB TYR A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 240 not shown) Planarity restraints: 381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 71 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 72 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 71 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 72 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 104 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.020 5.00e-02 4.00e+02 ... (remaining 378 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 504 2.77 - 3.30: 1610 3.30 - 3.83: 2713 3.83 - 4.37: 3259 4.37 - 4.90: 6117 Nonbonded interactions: 14203 Sorted by model distance: nonbonded pdb=" O SER A 39 " pdb=" OG SER A 39 " model vdw 2.233 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 71 " pdb=" OG1 THR A 71 " model vdw 2.396 3.040 nonbonded pdb=" O TYR B 41 " pdb=" OG SER B 44 " model vdw 2.410 3.040 nonbonded pdb=" O THR C 71 " pdb=" OG1 THR C 71 " model vdw 2.417 3.040 ... (remaining 14198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 92 or resid 94 through 124)) selection = (chain 'B' and (resid 34 through 92 or resid 94 through 124)) selection = (chain 'C' and (resid 34 through 92 or resid 94 through 124)) } 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=0.00 max=1.00 mean=0.99 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 5.310 Find NCS groups from input model: 0.020 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.009 0.044 2019 Z= 0.426 Angle : 0.847 5.552 2733 Z= 0.486 Chirality : 0.047 0.143 243 Planarity : 0.006 0.044 381 Dihedral : 11.510 65.851 705 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.09 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 2019) covalent geometry : angle 0.84714 ( 2733) hydrogen bonds : bond 0.44791 ( 10) hydrogen bonds : angle 8.69027 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0940 time to fit residues: 2.0168 Evaluate side-chains 15 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 93 GLN B A 103 GLN B 88 GLN B 93 GLN B B 103 GLN C 88 GLN C 94 GLN C 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078944 restraints weight = 9785.127| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.15 r_work: 0.3069 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2019 Z= 0.102 Angle : 0.561 4.156 2733 Z= 0.302 Chirality : 0.038 0.126 243 Planarity : 0.004 0.029 381 Dihedral : 4.224 15.620 315 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.37 % Allowed : 5.48 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.51 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR A 97 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 2019) covalent geometry : angle 0.56084 ( 2733) hydrogen bonds : bond 0.04609 ( 10) hydrogen bonds : angle 4.93614 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.077 Fit side-chains REVERT: B 103 GLN cc_start: 0.7764 (mt0) cc_final: 0.7530 (mt0) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.1348 time to fit residues: 2.6425 Evaluate side-chains 17 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.099625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076788 restraints weight = 7416.236| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.62 r_work: 0.3022 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2019 Z= 0.215 Angle : 0.662 5.212 2733 Z= 0.360 Chirality : 0.041 0.148 243 Planarity : 0.004 0.031 381 Dihedral : 4.547 15.713 315 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.74 % Allowed : 6.85 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.44 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 2019) covalent geometry : angle 0.66154 ( 2733) hydrogen bonds : bond 0.06786 ( 10) hydrogen bonds : angle 4.71363 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.042 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.0864 time to fit residues: 1.6596 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.100212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076565 restraints weight = 11583.051| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.34 r_work: 0.2996 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2019 Z= 0.172 Angle : 0.623 4.879 2733 Z= 0.337 Chirality : 0.040 0.153 243 Planarity : 0.004 0.028 381 Dihedral : 4.354 15.313 315 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.74 % Allowed : 8.22 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2019) covalent geometry : angle 0.62324 ( 2733) hydrogen bonds : bond 0.05678 ( 10) hydrogen bonds : angle 4.89198 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.086 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.0750 time to fit residues: 1.4867 Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5020 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.105245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081393 restraints weight = 12569.339| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.54 r_work: 0.3094 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2019 Z= 0.078 Angle : 0.492 3.754 2733 Z= 0.261 Chirality : 0.035 0.116 243 Planarity : 0.003 0.020 381 Dihedral : 3.529 13.723 315 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.91 % Allowed : 11.42 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 97 Details of bonding type rmsd covalent geometry : bond 0.00152 ( 2019) covalent geometry : angle 0.49242 ( 2733) hydrogen bonds : bond 0.02839 ( 10) hydrogen bonds : angle 4.70948 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.068 Fit side-chains REVERT: B 103 GLN cc_start: 0.7807 (mt0) cc_final: 0.7548 (mt0) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1858 time to fit residues: 3.0032 Evaluate side-chains 14 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.100997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077918 restraints weight = 8893.466| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.92 r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2019 Z= 0.146 Angle : 0.572 4.304 2733 Z= 0.307 Chirality : 0.037 0.122 243 Planarity : 0.003 0.021 381 Dihedral : 3.985 14.633 315 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.28 % Allowed : 10.50 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR B 97 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2019) covalent geometry : angle 0.57212 ( 2733) hydrogen bonds : bond 0.04983 ( 10) hydrogen bonds : angle 4.92506 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.076 Fit side-chains REVERT: A 90 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (p) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.1045 time to fit residues: 1.9101 Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.101019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077673 restraints weight = 10494.086| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.17 r_work: 0.3027 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2019 Z= 0.149 Angle : 0.586 4.595 2733 Z= 0.315 Chirality : 0.038 0.139 243 Planarity : 0.003 0.020 381 Dihedral : 4.031 14.564 315 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.28 % Allowed : 10.96 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2019) covalent geometry : angle 0.58631 ( 2733) hydrogen bonds : bond 0.05011 ( 10) hydrogen bonds : angle 5.02520 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.073 Fit side-chains REVERT: A 90 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8288 (p) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.0899 time to fit residues: 1.6300 Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.0020 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.101404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077896 restraints weight = 11802.103| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.38 r_work: 0.3023 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2019 Z= 0.129 Angle : 0.565 4.437 2733 Z= 0.302 Chirality : 0.037 0.132 243 Planarity : 0.003 0.019 381 Dihedral : 3.934 14.131 315 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 10.96 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR A 91 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2019) covalent geometry : angle 0.56514 ( 2733) hydrogen bonds : bond 0.04589 ( 10) hydrogen bonds : angle 5.00573 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.069 Fit side-chains REVERT: A 90 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8283 (p) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.1028 time to fit residues: 1.8716 Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076333 restraints weight = 12359.719| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.37 r_work: 0.2994 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2019 Z= 0.194 Angle : 0.632 5.240 2733 Z= 0.341 Chirality : 0.040 0.158 243 Planarity : 0.003 0.021 381 Dihedral : 4.239 14.568 315 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.20 % Allowed : 10.05 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2019) covalent geometry : angle 0.63227 ( 2733) hydrogen bonds : bond 0.05663 ( 10) hydrogen bonds : angle 5.19029 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.077 Fit side-chains REVERT: A 90 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8201 (p) outliers start: 7 outliers final: 5 residues processed: 16 average time/residue: 0.1019 time to fit residues: 1.8667 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077238 restraints weight = 9852.183| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.10 r_work: 0.3023 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2019 Z= 0.161 Angle : 0.600 4.844 2733 Z= 0.322 Chirality : 0.039 0.150 243 Planarity : 0.003 0.021 381 Dihedral : 4.134 14.521 315 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 10.96 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 38 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2019) covalent geometry : angle 0.60033 ( 2733) hydrogen bonds : bond 0.05201 ( 10) hydrogen bonds : angle 5.13912 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.072 Fit side-chains REVERT: A 90 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8220 (p) outliers start: 6 outliers final: 5 residues processed: 16 average time/residue: 0.0885 time to fit residues: 1.6346 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.102313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078570 restraints weight = 12655.323| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.51 r_work: 0.3031 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2019 Z= 0.101 Angle : 0.537 4.356 2733 Z= 0.285 Chirality : 0.036 0.121 243 Planarity : 0.003 0.019 381 Dihedral : 3.783 13.703 315 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.28 % Allowed : 11.42 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 97 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 2019) covalent geometry : angle 0.53728 ( 2733) hydrogen bonds : bond 0.03941 ( 10) hydrogen bonds : angle 4.94832 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 743.99 seconds wall clock time: 13 minutes 28.68 seconds (808.68 seconds total)