Starting phenix.real_space_refine on Tue Feb 3 12:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kty_62570/02_2026/9kty_62570.map" } resolution = 3.36 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= 0.000 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 S 6 5.16 5 C 726 2.51 5 N 210 2.21 5 O 222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1164 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "E" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "D" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "F" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 194 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Time building chain proxies: 0.28, per 1000 atoms: 0.24 Number of scatterers: 1164 At special positions: 0 Unit cell: (49, 89, 30, 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) S 6 16.00 O 222 8.00 N 210 7.00 C 726 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: 0.09 Conformation dependent library (CDL) restraints added in 38.1 milliseconds 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.560A pdb=" N THR C 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 35 " --> pdb=" O GLN A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.663A pdb=" N THR E 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 390 1.34 - 1.46: 313 1.46 - 1.57: 491 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 1206 Sorted by residual: bond pdb=" CG PRO D 40 " pdb=" CD PRO D 40 " ideal model delta sigma weight residual 1.503 1.489 0.014 3.40e-02 8.65e+02 1.81e-01 bond pdb=" CG PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 1.503 1.489 0.014 3.40e-02 8.65e+02 1.81e-01 bond pdb=" CG PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 1.503 1.489 0.014 3.40e-02 8.65e+02 1.79e-01 bond pdb=" CG PRO A 40 " pdb=" CD PRO A 40 " ideal model delta sigma weight residual 1.503 1.489 0.014 3.40e-02 8.65e+02 1.74e-01 bond pdb=" CG PRO C 40 " pdb=" CD PRO C 40 " ideal model delta sigma weight residual 1.503 1.489 0.014 3.40e-02 8.65e+02 1.68e-01 ... (remaining 1201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.64: 1452 0.64 - 1.27: 160 1.27 - 1.91: 8 1.91 - 2.55: 12 2.55 - 3.19: 12 Bond angle restraints: 1644 Sorted by residual: angle pdb=" N ALA C 26 " pdb=" CA ALA C 26 " pdb=" C ALA C 26 " ideal model delta sigma weight residual 108.32 111.00 -2.68 1.64e+00 3.72e-01 2.67e+00 angle pdb=" N ALA F 26 " pdb=" CA ALA F 26 " pdb=" C ALA F 26 " ideal model delta sigma weight residual 108.32 110.97 -2.65 1.64e+00 3.72e-01 2.61e+00 angle pdb=" N ALA E 26 " pdb=" CA ALA E 26 " pdb=" C ALA E 26 " ideal model delta sigma weight residual 108.32 110.94 -2.62 1.64e+00 3.72e-01 2.55e+00 angle pdb=" N ALA B 26 " pdb=" CA ALA B 26 " pdb=" C ALA B 26 " ideal model delta sigma weight residual 108.32 110.93 -2.61 1.64e+00 3.72e-01 2.53e+00 angle pdb=" N ALA A 26 " pdb=" CA ALA A 26 " pdb=" C ALA A 26 " ideal model delta sigma weight residual 108.32 110.93 -2.61 1.64e+00 3.72e-01 2.53e+00 ... (remaining 1639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.32: 468 7.32 - 14.65: 96 14.65 - 21.97: 48 21.97 - 29.29: 30 29.29 - 36.61: 12 Dihedral angle restraints: 654 sinusoidal: 252 harmonic: 402 Sorted by residual: dihedral pdb=" CA MET F 42 " pdb=" CB MET F 42 " pdb=" CG MET F 42 " pdb=" SD MET F 42 " ideal model delta sinusoidal sigma weight residual -60.00 -95.68 35.68 3 1.50e+01 4.44e-03 6.13e+00 dihedral pdb=" CA MET A 42 " pdb=" CB MET A 42 " pdb=" CG MET A 42 " pdb=" SD MET A 42 " ideal model delta sinusoidal sigma weight residual -60.00 -95.66 35.66 3 1.50e+01 4.44e-03 6.12e+00 dihedral pdb=" CA MET C 42 " pdb=" CB MET C 42 " pdb=" CG MET C 42 " pdb=" SD MET C 42 " ideal model delta sinusoidal sigma weight residual -60.00 -95.62 35.62 3 1.50e+01 4.44e-03 6.11e+00 ... (remaining 651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 46 0.019 - 0.037: 56 0.037 - 0.056: 25 0.056 - 0.074: 5 0.074 - 0.093: 6 Chirality restraints: 138 Sorted by residual: chirality pdb=" CA PHE C 32 " pdb=" N PHE C 32 " pdb=" C PHE C 32 " pdb=" CB PHE C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.14e-01 chirality pdb=" CA PHE A 32 " pdb=" N PHE A 32 " pdb=" C PHE A 32 " pdb=" CB PHE A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.05e-01 chirality pdb=" CA PHE F 32 " pdb=" N PHE F 32 " pdb=" C PHE F 32 " pdb=" CB PHE F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 135 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 43 " 0.010 5.00e-02 4.00e+02 1.45e-02 3.35e-01 pdb=" N PRO C 44 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO C 44 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO C 44 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 43 " 0.009 5.00e-02 4.00e+02 1.44e-02 3.32e-01 pdb=" N PRO D 44 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO D 44 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO D 44 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 43 " 0.009 5.00e-02 4.00e+02 1.43e-02 3.26e-01 pdb=" N PRO B 44 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.008 5.00e-02 4.00e+02 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 357 2.83 - 3.35: 1018 3.35 - 3.86: 1933 3.86 - 4.38: 2180 4.38 - 4.90: 4132 Nonbonded interactions: 9620 Sorted by model distance: nonbonded pdb=" NE2 GLN C 36 " pdb=" O GLN F 34 " model vdw 2.310 3.120 nonbonded pdb=" NE2 GLN B 36 " pdb=" O GLN E 34 " model vdw 2.363 3.120 nonbonded pdb=" O GLN B 34 " pdb=" NE2 GLN F 36 " model vdw 2.410 3.120 nonbonded pdb=" NE2 GLN A 36 " pdb=" O GLN D 34 " model vdw 2.456 3.120 nonbonded pdb=" O GLN A 34 " pdb=" NE2 GLN E 36 " model vdw 2.526 3.120 ... (remaining 9615 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' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.002 0.014 1206 Z= 0.094 Angle : 0.487 3.187 1644 Z= 0.263 Chirality : 0.035 0.093 138 Planarity : 0.003 0.014 228 Dihedral : 13.360 36.613 402 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.69 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR A 46 PHE 0.002 0.001 PHE C 32 TRP 0.004 0.001 TRP E 27 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 1206) covalent geometry : angle 0.48657 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.028 Fit side-chains REVERT: D 34 GLN cc_start: 0.8625 (pt0) cc_final: 0.8376 (pt0) REVERT: F 34 GLN cc_start: 0.8601 (pt0) cc_final: 0.8344 (pt0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0180 time to fit residues: 0.6718 Evaluate side-chains 24 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.130354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.120907 restraints weight = 1927.586| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.64 r_work: 0.3947 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1206 Z= 0.227 Angle : 0.540 3.551 1644 Z= 0.293 Chirality : 0.041 0.105 138 Planarity : 0.004 0.023 228 Dihedral : 5.030 14.560 150 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.12 % Favored : 81.88 % Rotamer: Outliers : 7.89 % Allowed : 7.89 % Favored : 84.21 % 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: -6.09 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR D 46 PHE 0.011 0.002 PHE E 32 TRP 0.007 0.002 TRP F 27 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 1206) covalent geometry : angle 0.54044 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.046 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 25 average time/residue: 0.0259 time to fit residues: 0.8643 Evaluate side-chains 33 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.128831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.119485 restraints weight = 1850.894| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.51 r_work: 0.3950 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1206 Z= 0.196 Angle : 0.516 3.357 1644 Z= 0.276 Chirality : 0.041 0.104 138 Planarity : 0.003 0.021 228 Dihedral : 5.080 16.034 150 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 7.89 % Allowed : 19.30 % Favored : 72.81 % 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: -6.12 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.66 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 46 PHE 0.009 0.001 PHE E 32 TRP 0.008 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 1206) covalent geometry : angle 0.51645 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.042 Fit side-chains REVERT: B 34 GLN cc_start: 0.9043 (pt0) cc_final: 0.8605 (pt0) outliers start: 9 outliers final: 8 residues processed: 27 average time/residue: 0.0254 time to fit residues: 0.8812 Evaluate side-chains 36 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.129393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.118866 restraints weight = 1824.306| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.82 r_work: 0.4000 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1206 Z= 0.131 Angle : 0.475 3.276 1644 Z= 0.249 Chirality : 0.039 0.100 138 Planarity : 0.003 0.019 228 Dihedral : 4.855 16.044 150 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.02 % Allowed : 20.18 % Favored : 72.81 % 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: -6.00 (0.31), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.24), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR E 46 PHE 0.007 0.001 PHE E 32 TRP 0.008 0.001 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 1206) covalent geometry : angle 0.47530 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.038 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 26 average time/residue: 0.0169 time to fit residues: 0.5617 Evaluate side-chains 28 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain F residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN F 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.125657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.115652 restraints weight = 1783.466| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.67 r_work: 0.3975 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1206 Z= 0.199 Angle : 0.521 4.061 1644 Z= 0.278 Chirality : 0.040 0.103 138 Planarity : 0.003 0.019 228 Dihedral : 5.083 16.863 150 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 9.65 % Allowed : 14.91 % Favored : 75.44 % 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: -6.13 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 46 PHE 0.011 0.002 PHE A 32 TRP 0.007 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 1206) covalent geometry : angle 0.52125 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.042 Fit side-chains REVERT: D 34 GLN cc_start: 0.8963 (pt0) cc_final: 0.8564 (pt0) outliers start: 11 outliers final: 10 residues processed: 28 average time/residue: 0.0282 time to fit residues: 0.9950 Evaluate side-chains 32 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN F 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.127855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.118003 restraints weight = 1894.157| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.61 r_work: 0.3953 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1206 Z= 0.224 Angle : 0.540 4.078 1644 Z= 0.289 Chirality : 0.041 0.105 138 Planarity : 0.003 0.020 228 Dihedral : 5.243 16.861 150 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 9.65 % Allowed : 15.79 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.22 (0.29), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.22), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 46 PHE 0.010 0.001 PHE A 32 TRP 0.008 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 1206) covalent geometry : angle 0.53993 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.040 Fit side-chains REVERT: B 34 GLN cc_start: 0.9138 (pt0) cc_final: 0.8768 (pt0) REVERT: D 34 GLN cc_start: 0.9004 (pt0) cc_final: 0.8753 (pt0) outliers start: 11 outliers final: 10 residues processed: 27 average time/residue: 0.0246 time to fit residues: 0.8519 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN F 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.128983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.118994 restraints weight = 1864.236| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.61 r_work: 0.3965 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1206 Z= 0.182 Angle : 0.507 3.981 1644 Z= 0.269 Chirality : 0.040 0.102 138 Planarity : 0.003 0.018 228 Dihedral : 5.131 16.480 150 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 9.65 % Allowed : 15.79 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.16 (0.29), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 46 PHE 0.009 0.001 PHE A 32 TRP 0.008 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 1206) covalent geometry : angle 0.50749 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.043 Fit side-chains REVERT: B 34 GLN cc_start: 0.9142 (pt0) cc_final: 0.8750 (pt0) REVERT: D 34 GLN cc_start: 0.9003 (pt0) cc_final: 0.8753 (pt0) outliers start: 11 outliers final: 9 residues processed: 27 average time/residue: 0.0265 time to fit residues: 0.9152 Evaluate side-chains 33 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN A 34 GLN F 29 GLN F 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.128015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.117263 restraints weight = 1755.836| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.76 r_work: 0.4000 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1206 Z= 0.138 Angle : 0.469 3.568 1644 Z= 0.247 Chirality : 0.039 0.099 138 Planarity : 0.003 0.019 228 Dihedral : 4.922 15.449 150 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 9.65 % Allowed : 15.79 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.02 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 46 PHE 0.009 0.001 PHE A 32 TRP 0.009 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 1206) covalent geometry : angle 0.46947 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.046 Fit side-chains REVERT: B 34 GLN cc_start: 0.9062 (pt0) cc_final: 0.8628 (pt0) outliers start: 11 outliers final: 9 residues processed: 26 average time/residue: 0.0211 time to fit residues: 0.7092 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN A 34 GLN D 34 GLN F 29 GLN F 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.130526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.120225 restraints weight = 1799.118| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.66 r_work: 0.3976 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1206 Z= 0.184 Angle : 0.510 3.906 1644 Z= 0.272 Chirality : 0.040 0.102 138 Planarity : 0.003 0.018 228 Dihedral : 5.066 16.011 150 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 8.77 % Allowed : 16.67 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.03 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 46 PHE 0.008 0.001 PHE A 32 TRP 0.007 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 1206) covalent geometry : angle 0.50975 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.044 Fit side-chains REVERT: B 34 GLN cc_start: 0.9093 (pt0) cc_final: 0.8833 (pt0) outliers start: 10 outliers final: 10 residues processed: 27 average time/residue: 0.0262 time to fit residues: 0.9049 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN F 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.125594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.115787 restraints weight = 1719.916| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.54 r_work: 0.3975 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1206 Z= 0.190 Angle : 0.510 3.856 1644 Z= 0.273 Chirality : 0.040 0.102 138 Planarity : 0.003 0.018 228 Dihedral : 5.118 16.211 150 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 7.89 % Allowed : 19.30 % Favored : 72.81 % 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: -6.02 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 46 PHE 0.007 0.001 PHE A 32 TRP 0.007 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 1206) covalent geometry : angle 0.51020 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 276 Ramachandran restraints generated. 138 Oldfield, 0 Emsley, 138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.046 Fit side-chains REVERT: B 34 GLN cc_start: 0.9113 (pt0) cc_final: 0.8823 (pt0) outliers start: 9 outliers final: 9 residues processed: 27 average time/residue: 0.0262 time to fit residues: 0.9040 Evaluate side-chains 34 residues out of total 114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.129589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.119575 restraints weight = 1819.437| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.62 r_work: 0.3972 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1206 Z= 0.183 Angle : 0.504 3.920 1644 Z= 0.268 Chirality : 0.040 0.102 138 Planarity : 0.003 0.018 228 Dihedral : 5.114 16.374 150 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 7.89 % Allowed : 19.30 % Favored : 72.81 % 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: -6.00 (0.30), residues: 138 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.23), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 46 PHE 0.008 0.001 PHE A 32 TRP 0.008 0.002 TRP D 27 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 1206) covalent geometry : angle 0.50403 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 662.46 seconds wall clock time: 12 minutes 8.64 seconds (728.64 seconds total)