Starting phenix.real_space_refine on Tue Mar 3 10:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2026/7m61_23686.map" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 1.000 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: 3 Type Number sf(0) Gaussians C 1030 2.51 5 N 305 2.21 5 O 355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 1690 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 152 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.25, per 1000 atoms: 0.15 Number of scatterers: 1690 At special positions: 0 Unit cell: (59.08, 51.695, 48.53, 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 355 8.00 N 305 7.00 C 1030 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 46.7 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 15 removed outlier: 7.243A pdb=" N ASN A 14 " --> pdb=" O PHE G 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.100A pdb=" N ASN A 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.755A pdb=" N ALA F 25 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA H 25 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE B 23 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA J 25 " --> pdb=" O GLY B 24 " (cutoff:3.500A) 9 hydrogen bonds defined for protein. 27 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.20 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 275 1.29 - 1.35: 293 1.35 - 1.42: 232 1.42 - 1.48: 250 1.48 - 1.55: 655 Bond restraints: 1705 Sorted by residual: bond pdb=" CB ILE E 26 " pdb=" CG1 ILE E 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CB ILE I 26 " pdb=" CG1 ILE I 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE C 26 " pdb=" CG1 ILE C 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE G 26 " pdb=" CG1 ILE G 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" CB ILE A 26 " pdb=" CG1 ILE A 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 2236 1.84 - 3.69: 59 3.69 - 5.53: 0 5.53 - 7.38: 5 7.38 - 9.22: 15 Bond angle restraints: 2315 Sorted by residual: angle pdb=" CG1 ILE A 26 " pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 110.70 101.48 9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" CG1 ILE I 26 " pdb=" CB ILE I 26 " pdb=" CG2 ILE I 26 " ideal model delta sigma weight residual 110.70 101.49 9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" CG1 ILE G 26 " pdb=" CB ILE G 26 " pdb=" CG2 ILE G 26 " ideal model delta sigma weight residual 110.70 101.51 9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" CG1 ILE E 26 " pdb=" CB ILE E 26 " pdb=" CG2 ILE E 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" CG1 ILE C 26 " pdb=" CB ILE C 26 " pdb=" CG2 ILE C 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.35e+00 ... (remaining 2310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.63: 780 8.63 - 17.25: 90 17.25 - 25.87: 40 25.87 - 34.50: 20 34.50 - 43.12: 20 Dihedral angle restraints: 950 sinusoidal: 300 harmonic: 650 Sorted by residual: dihedral pdb=" CA PHE I 15 " pdb=" C PHE I 15 " pdb=" N LEU I 16 " pdb=" CA LEU I 16 " ideal model delta harmonic sigma weight residual 180.00 167.01 12.99 0 5.00e+00 4.00e-02 6.75e+00 dihedral pdb=" CA PHE G 15 " pdb=" C PHE G 15 " pdb=" N LEU G 16 " pdb=" CA LEU G 16 " ideal model delta harmonic sigma weight residual 180.00 167.04 12.96 0 5.00e+00 4.00e-02 6.72e+00 dihedral pdb=" CA PHE A 15 " pdb=" C PHE A 15 " pdb=" N LEU A 16 " pdb=" CA LEU A 16 " ideal model delta harmonic sigma weight residual 180.00 167.07 12.93 0 5.00e+00 4.00e-02 6.69e+00 ... (remaining 947 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 200 0.061 - 0.121: 51 0.121 - 0.181: 9 0.181 - 0.241: 10 0.241 - 0.301: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU D 27 " pdb=" CB LEU D 27 " pdb=" CD1 LEU D 27 " pdb=" CD2 LEU D 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU F 27 " pdb=" CB LEU F 27 " pdb=" CD1 LEU F 27 " pdb=" CD2 LEU F 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 272 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR J 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR F 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR B 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 291 2.75 - 3.29: 1811 3.29 - 3.83: 2864 3.83 - 4.36: 3257 4.36 - 4.90: 6142 Nonbonded interactions: 14365 Sorted by model distance: nonbonded pdb=" O SER E 34 " pdb=" OG SER G 34 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 34 " pdb=" OG SER I 34 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 34 " pdb=" O SER G 34 " model vdw 2.218 3.040 nonbonded pdb=" O SER C 34 " pdb=" OG SER E 34 " model vdw 2.218 3.040 nonbonded pdb=" ND2 ASN G 22 " pdb=" O GLY G 24 " model vdw 2.433 3.120 ... (remaining 14360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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 group one per residue 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: 0.090 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.070 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:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 0.102 1715 Z= 0.803 Angle : 1.018 9.221 2315 Z= 0.508 Chirality : 0.076 0.301 275 Planarity : 0.003 0.017 300 Dihedral : 12.788 43.118 530 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -4.63 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.006 TYR J 37 PHE 0.005 0.001 PHE H 23 HIS 0.002 0.001 HIS G 18 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 1705) covalent geometry : angle 1.01805 ( 2315) hydrogen bonds : bond 0.29472 ( 9) hydrogen bonds : angle 8.68358 ( 27) Misc. bond : bond 0.10166 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0214 time to fit residues: 1.2011 Evaluate side-chains 21 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 9.9990 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.099891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.086004 restraints weight = 5140.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088166 restraints weight = 2731.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.089546 restraints weight = 1854.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090217 restraints weight = 1437.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.090959 restraints weight = 1243.810| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1715 Z= 0.142 Angle : 0.714 8.316 2315 Z= 0.351 Chirality : 0.048 0.154 275 Planarity : 0.002 0.010 300 Dihedral : 4.784 13.842 230 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % 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: -4.98 (0.29), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.22), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR H 37 PHE 0.011 0.001 PHE F 23 HIS 0.001 0.000 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 1705) covalent geometry : angle 0.71441 ( 2315) hydrogen bonds : bond 0.06228 ( 9) hydrogen bonds : angle 5.19114 ( 27) Misc. bond : bond 0.00032 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.046 Fit side-chains REVERT: B 29 SER cc_start: 0.9020 (t) cc_final: 0.8781 (p) REVERT: E 15 PHE cc_start: 0.8293 (m-10) cc_final: 0.7996 (m-80) REVERT: H 23 PHE cc_start: 0.8348 (m-80) cc_final: 0.7947 (m-80) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.0226 time to fit residues: 1.3886 Evaluate side-chains 28 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.098096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.085142 restraints weight = 5285.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.087114 restraints weight = 2895.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088459 restraints weight = 2029.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089315 restraints weight = 1587.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089318 restraints weight = 1343.647| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1715 Z= 0.154 Angle : 0.741 9.527 2315 Z= 0.355 Chirality : 0.048 0.202 275 Planarity : 0.003 0.010 300 Dihedral : 5.239 15.161 230 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 5.13 % Allowed : 14.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.95 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR H 37 PHE 0.010 0.002 PHE F 23 HIS 0.002 0.000 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 1705) covalent geometry : angle 0.74094 ( 2315) hydrogen bonds : bond 0.06004 ( 9) hydrogen bonds : angle 4.99551 ( 27) Misc. bond : bond 0.00070 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.040 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 29 average time/residue: 0.0199 time to fit residues: 0.7971 Evaluate side-chains 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.098774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086008 restraints weight = 5226.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087773 restraints weight = 3081.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.089034 restraints weight = 2226.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.089645 restraints weight = 1776.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090370 restraints weight = 1569.508| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1715 Z= 0.170 Angle : 0.678 8.333 2315 Z= 0.342 Chirality : 0.045 0.143 275 Planarity : 0.002 0.008 300 Dihedral : 5.458 14.101 230 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 6.67 % Allowed : 17.95 % Favored : 75.38 % 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: -4.91 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR H 37 PHE 0.010 0.002 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 1705) covalent geometry : angle 0.67802 ( 2315) hydrogen bonds : bond 0.04939 ( 9) hydrogen bonds : angle 4.54226 ( 27) Misc. bond : bond 0.00033 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 32 average time/residue: 0.0223 time to fit residues: 1.0152 Evaluate side-chains 25 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.099777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086661 restraints weight = 5298.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088435 restraints weight = 3137.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.089777 restraints weight = 2276.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.090470 restraints weight = 1836.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.090470 restraints weight = 1597.354| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1715 Z= 0.178 Angle : 0.675 8.685 2315 Z= 0.344 Chirality : 0.045 0.132 275 Planarity : 0.002 0.009 300 Dihedral : 5.537 15.880 230 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 7.18 % Allowed : 22.05 % Favored : 70.77 % 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: -4.98 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR H 37 PHE 0.012 0.002 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 1705) covalent geometry : angle 0.67516 ( 2315) hydrogen bonds : bond 0.04836 ( 9) hydrogen bonds : angle 4.43792 ( 27) Misc. bond : bond 0.00037 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8948 (p0) REVERT: J 37 TYR cc_start: 0.7780 (m-10) cc_final: 0.4763 (p90) outliers start: 14 outliers final: 9 residues processed: 27 average time/residue: 0.0224 time to fit residues: 0.8396 Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 overall best weight: 6.7790 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.105977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092968 restraints weight = 5065.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095009 restraints weight = 2891.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096540 restraints weight = 2037.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.097348 restraints weight = 1588.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.098054 restraints weight = 1365.721| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1715 Z= 0.171 Angle : 0.685 7.712 2315 Z= 0.344 Chirality : 0.045 0.198 275 Planarity : 0.002 0.009 300 Dihedral : 5.456 14.886 230 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 6.15 % Allowed : 22.56 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.97 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR H 37 PHE 0.014 0.002 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 1705) covalent geometry : angle 0.68529 ( 2315) hydrogen bonds : bond 0.04364 ( 9) hydrogen bonds : angle 4.31184 ( 27) Misc. bond : bond 0.00030 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 26 average time/residue: 0.0239 time to fit residues: 0.8895 Evaluate side-chains 29 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 20.0000 chunk 18 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 0.0000 chunk 16 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 overall best weight: 5.0792 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.108551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.095456 restraints weight = 4878.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097705 restraints weight = 2792.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098739 restraints weight = 1936.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.099948 restraints weight = 1584.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100399 restraints weight = 1324.813| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1715 Z= 0.140 Angle : 0.640 7.770 2315 Z= 0.317 Chirality : 0.043 0.176 275 Planarity : 0.002 0.008 300 Dihedral : 5.037 14.229 230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 7.69 % Allowed : 21.54 % Favored : 70.77 % 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 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR H 37 PHE 0.012 0.001 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 1705) covalent geometry : angle 0.64045 ( 2315) hydrogen bonds : bond 0.03981 ( 9) hydrogen bonds : angle 3.98901 ( 27) Misc. bond : bond 0.00025 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8903 (p0) outliers start: 15 outliers final: 11 residues processed: 29 average time/residue: 0.0240 time to fit residues: 0.9945 Evaluate side-chains 31 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.109163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095825 restraints weight = 5070.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.097982 restraints weight = 2926.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.099457 restraints weight = 2055.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100286 restraints weight = 1614.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.101086 restraints weight = 1389.127| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1715 Z= 0.141 Angle : 0.669 9.086 2315 Z= 0.325 Chirality : 0.046 0.244 275 Planarity : 0.002 0.008 300 Dihedral : 5.063 15.403 230 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 7.18 % Allowed : 21.54 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.98 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR H 37 PHE 0.011 0.001 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 1705) covalent geometry : angle 0.66865 ( 2315) hydrogen bonds : bond 0.04026 ( 9) hydrogen bonds : angle 3.92201 ( 27) Misc. bond : bond 0.00024 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8944 (p0) outliers start: 14 outliers final: 11 residues processed: 29 average time/residue: 0.0213 time to fit residues: 0.9083 Evaluate side-chains 30 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.105946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092850 restraints weight = 5305.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094683 restraints weight = 3030.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.096259 restraints weight = 2167.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097059 restraints weight = 1699.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.097599 restraints weight = 1463.246| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1715 Z= 0.213 Angle : 0.725 8.771 2315 Z= 0.371 Chirality : 0.049 0.219 275 Planarity : 0.003 0.009 300 Dihedral : 5.789 16.742 230 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 7.69 % Allowed : 20.51 % Favored : 71.79 % 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: -4.99 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR H 37 PHE 0.013 0.002 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 1705) covalent geometry : angle 0.72541 ( 2315) hydrogen bonds : bond 0.04539 ( 9) hydrogen bonds : angle 4.05638 ( 27) Misc. bond : bond 0.00039 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 29 average time/residue: 0.0247 time to fit residues: 1.0197 Evaluate side-chains 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 overall best weight: 6.2186 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.108798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.095922 restraints weight = 5041.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.097721 restraints weight = 2875.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.099234 restraints weight = 2058.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.100164 restraints weight = 1626.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.100185 restraints weight = 1379.831| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1715 Z= 0.163 Angle : 0.693 8.931 2315 Z= 0.348 Chirality : 0.047 0.221 275 Planarity : 0.002 0.007 300 Dihedral : 5.395 14.982 230 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 6.15 % Allowed : 21.54 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.02 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR H 37 PHE 0.011 0.002 PHE F 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 1705) covalent geometry : angle 0.69342 ( 2315) hydrogen bonds : bond 0.04056 ( 9) hydrogen bonds : angle 3.90246 ( 27) Misc. bond : bond 0.00028 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 27 average time/residue: 0.0241 time to fit residues: 0.9360 Evaluate side-chains 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.111076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.098021 restraints weight = 5074.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100190 restraints weight = 2871.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.101703 restraints weight = 1999.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102686 restraints weight = 1559.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.102915 restraints weight = 1311.041| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1715 Z= 0.127 Angle : 0.656 8.604 2315 Z= 0.323 Chirality : 0.045 0.219 275 Planarity : 0.002 0.009 300 Dihedral : 4.808 13.868 230 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 4.10 % Allowed : 23.59 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.05 (0.30), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.23), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR F 37 PHE 0.010 0.001 PHE F 23 HIS 0.001 0.000 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 1705) covalent geometry : angle 0.65612 ( 2315) hydrogen bonds : bond 0.03533 ( 9) hydrogen bonds : angle 3.70378 ( 27) Misc. bond : bond 0.00020 ( 10) =============================================================================== Job complete usr+sys time: 441.07 seconds wall clock time: 8 minutes 50.22 seconds (530.22 seconds total)