Starting phenix.real_space_refine on Wed Jul 1 20:45:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.map" model { file = "/net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obk_70294/07_2026/9obk_70294.cif" } resolution = 3.01 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= 0.002 sd= 0.009 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 10 5.16 5 C 1330 2.51 5 N 340 2.21 5 O 360 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 204 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SME:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.64, per 1000 atoms: 0.31 Number of scatterers: 2040 At special positions: 0 Unit cell: (53.535, 81.755, 40.67, 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 10 16.00 O 360 8.00 N 340 7.00 C 1330 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: 0.24 Conformation dependent library (CDL) restraints added in 96.1 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.499A pdb=" N LYS A 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE E 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS E 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE I 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 31 through 36 removed outlier: 6.271A pdb=" N ILE D 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU H 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY D 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL H 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SME D 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU D 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY A 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL D 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SME A 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 39 through 40 removed outlier: 6.483A pdb=" N VAL A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 16 through 19 removed outlier: 6.503A pdb=" N LYS C 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE G 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE C 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 31 through 36 removed outlier: 6.269A pdb=" N ILE B 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU F 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SME B 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE F 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU J 34 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY F 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL J 36 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SME F 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 39 through 40 removed outlier: 6.493A pdb=" N VAL C 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.29 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.33: 650 1.33 - 1.44: 160 1.44 - 1.55: 1230 1.55 - 1.65: 0 1.65 - 1.76: 20 Bond restraints: 2060 Sorted by residual: bond pdb=" CE SME D 35 " pdb=" S SME D 35 " ideal model delta sigma weight residual 1.804 1.731 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CE SME C 35 " pdb=" S SME C 35 " ideal model delta sigma weight residual 1.804 1.732 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CE SME E 35 " pdb=" S SME E 35 " ideal model delta sigma weight residual 1.804 1.732 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CE SME A 35 " pdb=" S SME A 35 " ideal model delta sigma weight residual 1.804 1.732 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CE SME B 35 " pdb=" S SME B 35 " ideal model delta sigma weight residual 1.804 1.732 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 2055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 2300 0.75 - 1.51: 279 1.51 - 2.26: 101 2.26 - 3.01: 39 3.01 - 3.77: 41 Bond angle restraints: 2760 Sorted by residual: angle pdb=" N ASN J 27 " pdb=" CA ASN J 27 " pdb=" C ASN J 27 " ideal model delta sigma weight residual 112.26 109.24 3.02 1.32e+00 5.74e-01 5.22e+00 angle pdb=" N ASN F 27 " pdb=" CA ASN F 27 " pdb=" C ASN F 27 " ideal model delta sigma weight residual 112.26 109.25 3.01 1.32e+00 5.74e-01 5.19e+00 angle pdb=" N ASN H 27 " pdb=" CA ASN H 27 " pdb=" C ASN H 27 " ideal model delta sigma weight residual 112.26 109.26 3.00 1.32e+00 5.74e-01 5.18e+00 angle pdb=" N ASN B 27 " pdb=" CA ASN B 27 " pdb=" C ASN B 27 " ideal model delta sigma weight residual 112.26 109.27 2.99 1.32e+00 5.74e-01 5.14e+00 angle pdb=" N ASN I 27 " pdb=" CA ASN I 27 " pdb=" C ASN I 27 " ideal model delta sigma weight residual 112.26 109.28 2.98 1.32e+00 5.74e-01 5.10e+00 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.85: 902 7.85 - 15.69: 158 15.69 - 23.54: 60 23.54 - 31.39: 10 31.39 - 39.23: 70 Dihedral angle restraints: 1200 sinusoidal: 470 harmonic: 730 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" CB LEU J 34 " pdb=" CG LEU J 34 " pdb=" CD1 LEU J 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.96 33.04 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.97 33.03 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU I 34 " pdb=" CB LEU I 34 " pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sinusoidal sigma weight residual 180.00 146.98 33.02 3 1.50e+01 4.44e-03 5.49e+00 ... (remaining 1197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 162 0.024 - 0.047: 88 0.047 - 0.071: 10 0.071 - 0.094: 38 0.094 - 0.118: 32 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE C 31 " pdb=" N ILE C 31 " pdb=" C ILE C 31 " pdb=" CB ILE C 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 327 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 19 " -0.004 2.00e-02 2.50e+03 3.13e-03 1.72e-01 pdb=" CG PHE G 19 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE G 19 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 19 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 19 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 21 " 0.002 2.00e-02 2.50e+03 4.09e-03 1.68e-01 pdb=" C ALA D 21 " -0.007 2.00e-02 2.50e+03 pdb=" O ALA D 21 " 0.003 2.00e-02 2.50e+03 pdb=" N GLU D 22 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 21 " 0.002 2.00e-02 2.50e+03 4.09e-03 1.67e-01 pdb=" C ALA I 21 " -0.007 2.00e-02 2.50e+03 pdb=" O ALA I 21 " 0.003 2.00e-02 2.50e+03 pdb=" N GLU I 22 " 0.002 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.09: 1402 3.09 - 3.54: 1875 3.54 - 3.99: 3083 3.99 - 4.45: 3622 4.45 - 4.90: 6835 Nonbonded interactions: 16817 Sorted by model distance: nonbonded pdb=" O GLY A 37 " pdb=" O GLY C 25 " model vdw 2.632 3.040 nonbonded pdb=" O GLY A 25 " pdb=" O GLY B 37 " model vdw 2.640 3.040 nonbonded pdb=" O GLY F 25 " pdb=" O GLY H 37 " model vdw 2.647 3.040 nonbonded pdb=" O GLY C 37 " pdb=" O GLY E 25 " model vdw 2.647 3.040 nonbonded pdb=" O GLY H 25 " pdb=" O GLY J 37 " model vdw 2.647 3.040 ... (remaining 16812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.780 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:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.008 0.073 2060 Z= 0.405 Angle : 0.766 3.765 2760 Z= 0.459 Chirality : 0.050 0.118 330 Planarity : 0.001 0.004 340 Dihedral : 14.233 39.234 740 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.19 (0.48), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE G 19 HIS 0.001 0.000 HIS I 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.41 ( 2060) covalent geometry : angle 0.76568 / 0.46 ( 2760) hydrogen bonds : bond 0.09884 / 7.16 ( 36) hydrogen bonds : angle 7.79014 / 5.21 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.097 Fit side-chains REVERT: B 28 LYS cc_start: 0.8649 (tttm) cc_final: 0.8392 (tttp) REVERT: G 28 LYS cc_start: 0.8671 (tttm) cc_final: 0.8351 (tppt) REVERT: I 28 LYS cc_start: 0.8635 (tttm) cc_final: 0.8382 (tppt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0646 time to fit residues: 5.0214 Evaluate side-chains 37 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.129522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.123630 restraints weight = 3862.314| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.64 r_work: 0.4174 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.017 2060 Z= 0.263 Angle : 0.596 3.979 2760 Z= 0.327 Chirality : 0.050 0.132 330 Planarity : 0.002 0.015 340 Dihedral : 14.673 52.123 340 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 7.00 % Allowed : 17.00 % Favored : 76.00 % 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: -1.05 (0.51), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 19 HIS 0.000 0.000 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 ( 2060) covalent geometry : angle 0.59572 / 0.33 ( 2760) hydrogen bonds : bond 0.01647 / 1.19 ( 36) hydrogen bonds : angle 4.51257 / 2.97 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.085 Fit side-chains REVERT: A 34 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9208 (mp) REVERT: B 34 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9208 (mp) REVERT: C 34 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9209 (mp) REVERT: D 34 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9383 (mp) REVERT: E 34 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9211 (mp) REVERT: F 34 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9325 (mp) REVERT: G 28 LYS cc_start: 0.8759 (tttm) cc_final: 0.8286 (tppt) REVERT: G 34 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9032 (mp) REVERT: H 34 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9220 (mp) REVERT: I 28 LYS cc_start: 0.8681 (tttm) cc_final: 0.8311 (tppt) REVERT: I 34 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9065 (mp) REVERT: J 34 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9200 (mp) outliers start: 14 outliers final: 3 residues processed: 54 average time/residue: 0.0732 time to fit residues: 4.4883 Evaluate side-chains 59 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN E 15 GLN H 15 GLN I 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.120763 restraints weight = 4002.265| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.60 r_work: 0.4077 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.022 2060 Z= 0.336 Angle : 0.641 4.052 2760 Z= 0.351 Chirality : 0.050 0.130 330 Planarity : 0.002 0.012 340 Dihedral : 14.931 48.059 340 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.00 % Allowed : 24.50 % Favored : 67.50 % 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: -1.27 (0.51), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE C 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.34 ( 2060) covalent geometry : angle 0.64124 / 0.35 ( 2760) hydrogen bonds : bond 0.01576 / 1.14 ( 36) hydrogen bonds : angle 3.86178 / 2.53 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.082 Fit side-chains REVERT: A 34 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9225 (mp) REVERT: B 34 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9223 (mp) REVERT: C 34 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9244 (mp) REVERT: D 34 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9403 (mp) REVERT: E 34 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9261 (mp) REVERT: F 34 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9332 (mp) REVERT: G 28 LYS cc_start: 0.8781 (tttm) cc_final: 0.8324 (tppt) REVERT: G 34 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9074 (mp) REVERT: H 34 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9185 (mp) REVERT: I 28 LYS cc_start: 0.8718 (tttm) cc_final: 0.8363 (tppt) REVERT: I 34 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9139 (mp) REVERT: J 22 GLU cc_start: 0.9080 (tt0) cc_final: 0.8799 (tt0) REVERT: J 34 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9153 (mp) outliers start: 16 outliers final: 5 residues processed: 49 average time/residue: 0.0727 time to fit residues: 4.0681 Evaluate side-chains 60 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.128140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.122237 restraints weight = 4006.942| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.64 r_work: 0.4104 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.020 2060 Z= 0.299 Angle : 0.608 3.827 2760 Z= 0.332 Chirality : 0.050 0.128 330 Planarity : 0.002 0.011 340 Dihedral : 14.670 47.569 340 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 8.00 % Allowed : 29.00 % Favored : 63.00 % 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: -1.42 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE C 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.30 ( 2060) covalent geometry : angle 0.60803 / 0.33 ( 2760) hydrogen bonds : bond 0.01350 / 0.97 ( 36) hydrogen bonds : angle 3.68788 / 2.40 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.098 Fit side-chains REVERT: A 34 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9184 (mp) REVERT: B 34 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9189 (mp) REVERT: C 34 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9238 (mp) REVERT: D 34 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9388 (mp) REVERT: E 34 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9236 (mp) REVERT: F 34 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9350 (mp) REVERT: G 28 LYS cc_start: 0.8769 (tttm) cc_final: 0.8293 (tppt) REVERT: G 34 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9027 (mp) REVERT: H 34 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9236 (mp) REVERT: I 28 LYS cc_start: 0.8698 (tttm) cc_final: 0.8331 (tppt) REVERT: I 34 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9121 (mp) REVERT: J 22 GLU cc_start: 0.9060 (tt0) cc_final: 0.8781 (tt0) REVERT: J 34 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9220 (mp) outliers start: 16 outliers final: 5 residues processed: 51 average time/residue: 0.0846 time to fit residues: 4.9017 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.124785 restraints weight = 3947.656| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.62 r_work: 0.4149 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4060 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 2060 Z= 0.228 Angle : 0.556 3.382 2760 Z= 0.303 Chirality : 0.050 0.125 330 Planarity : 0.002 0.010 340 Dihedral : 14.235 51.471 340 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.50 % Allowed : 29.00 % Favored : 63.50 % 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: -1.34 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 2060) covalent geometry : angle 0.55581 / 0.30 ( 2760) hydrogen bonds : bond 0.01187 / 0.85 ( 36) hydrogen bonds : angle 3.63691 / 2.36 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.079 Fit side-chains REVERT: A 34 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9198 (mp) REVERT: B 22 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: B 34 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9201 (mp) REVERT: C 34 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9232 (mp) REVERT: D 34 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9418 (mp) REVERT: E 34 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9193 (mp) REVERT: F 34 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9381 (mp) REVERT: G 28 LYS cc_start: 0.8779 (tttm) cc_final: 0.8293 (tppt) REVERT: G 34 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9008 (mp) REVERT: I 28 LYS cc_start: 0.8701 (tttm) cc_final: 0.8332 (tppt) REVERT: I 34 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9021 (mp) REVERT: J 22 GLU cc_start: 0.9011 (tt0) cc_final: 0.8736 (tt0) outliers start: 15 outliers final: 2 residues processed: 56 average time/residue: 0.0681 time to fit residues: 4.3669 Evaluate side-chains 62 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.128309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.122654 restraints weight = 3873.441| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.53 r_work: 0.4131 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.020 2060 Z= 0.293 Angle : 0.619 3.944 2760 Z= 0.332 Chirality : 0.050 0.126 330 Planarity : 0.002 0.010 340 Dihedral : 14.116 51.676 340 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 8.00 % Allowed : 29.00 % Favored : 63.00 % 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: -1.38 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 19 HIS 0.000 0.000 HIS J 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.29 ( 2060) covalent geometry : angle 0.61855 / 0.33 ( 2760) hydrogen bonds : bond 0.01344 / 0.97 ( 36) hydrogen bonds : angle 3.56193 / 2.33 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.078 Fit side-chains REVERT: A 34 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9210 (mp) REVERT: B 34 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9219 (mp) REVERT: C 34 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9264 (mp) REVERT: E 34 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9239 (mp) REVERT: G 28 LYS cc_start: 0.8780 (tttm) cc_final: 0.8295 (tppt) REVERT: G 34 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9038 (mp) REVERT: I 28 LYS cc_start: 0.8691 (tttm) cc_final: 0.8334 (tppt) REVERT: I 34 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9127 (mp) REVERT: J 34 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9264 (mt) outliers start: 16 outliers final: 7 residues processed: 50 average time/residue: 0.0707 time to fit residues: 4.0500 Evaluate side-chains 60 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.132791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.126955 restraints weight = 3829.992| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.67 r_work: 0.4229 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4140 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2060 Z= 0.120 Angle : 0.503 3.192 2760 Z= 0.274 Chirality : 0.050 0.123 330 Planarity : 0.001 0.010 340 Dihedral : 13.205 57.378 340 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.50 % Allowed : 30.50 % Favored : 63.00 % 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: -1.26 (0.48), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 19 HIS 0.000 0.000 HIS I 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2060) covalent geometry : angle 0.50279 / 0.27 ( 2760) hydrogen bonds : bond 0.00956 / 0.71 ( 36) hydrogen bonds : angle 3.60440 / 2.35 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.080 Fit side-chains REVERT: A 34 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8915 (mt) REVERT: B 22 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: B 34 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9033 (mt) REVERT: C 34 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9185 (mp) REVERT: D 34 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9416 (mt) REVERT: E 34 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9132 (mp) REVERT: F 34 LEU cc_start: 0.9533 (mp) cc_final: 0.9172 (mt) REVERT: G 28 LYS cc_start: 0.8701 (tttm) cc_final: 0.8183 (tppt) REVERT: G 34 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8985 (mp) REVERT: H 34 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9290 (mp) REVERT: I 28 LYS cc_start: 0.8654 (tttm) cc_final: 0.8238 (tppt) REVERT: I 34 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8989 (mp) REVERT: J 34 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9199 (mt) outliers start: 13 outliers final: 3 residues processed: 58 average time/residue: 0.0639 time to fit residues: 4.2646 Evaluate side-chains 68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.127714 restraints weight = 3803.392| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.64 r_work: 0.4190 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2060 Z= 0.168 Angle : 0.528 3.559 2760 Z= 0.287 Chirality : 0.050 0.123 330 Planarity : 0.001 0.009 340 Dihedral : 13.347 57.498 340 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.50 % Allowed : 32.50 % Favored : 61.00 % 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: -1.10 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE E 19 HIS 0.000 0.000 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 2060) covalent geometry : angle 0.52829 / 0.29 ( 2760) hydrogen bonds : bond 0.01108 / 0.79 ( 36) hydrogen bonds : angle 3.47073 / 2.27 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.078 Fit side-chains REVERT: A 34 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9022 (mt) REVERT: B 22 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: B 34 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9069 (mt) REVERT: C 34 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9195 (mp) REVERT: D 34 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9299 (mt) REVERT: E 34 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.8979 (mp) REVERT: F 34 LEU cc_start: 0.9515 (mp) cc_final: 0.9151 (mt) REVERT: G 28 LYS cc_start: 0.8739 (tttm) cc_final: 0.8241 (tppt) REVERT: G 34 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8988 (mp) REVERT: H 34 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9297 (mp) REVERT: I 28 LYS cc_start: 0.8687 (tttm) cc_final: 0.8301 (tppt) REVERT: I 34 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8992 (mp) REVERT: J 34 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9234 (mt) outliers start: 13 outliers final: 3 residues processed: 55 average time/residue: 0.0665 time to fit residues: 4.2068 Evaluate side-chains 64 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.127471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.121890 restraints weight = 3922.669| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.59 r_work: 0.4144 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.021 2060 Z= 0.254 Angle : 0.589 3.783 2760 Z= 0.316 Chirality : 0.050 0.125 330 Planarity : 0.002 0.010 340 Dihedral : 13.632 56.044 340 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.50 % Allowed : 33.00 % Favored : 60.50 % 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: -1.21 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 19 HIS 0.000 0.000 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 ( 2060) covalent geometry : angle 0.58922 / 0.32 ( 2760) hydrogen bonds : bond 0.01286 / 0.91 ( 36) hydrogen bonds : angle 3.44396 / 2.26 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.078 Fit side-chains REVERT: A 34 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9154 (mp) REVERT: B 34 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9214 (mp) REVERT: C 34 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9253 (mp) REVERT: D 34 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9365 (mt) REVERT: E 34 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9248 (mp) REVERT: F 34 LEU cc_start: 0.9532 (mp) cc_final: 0.9176 (mt) REVERT: G 28 LYS cc_start: 0.8759 (tttm) cc_final: 0.8277 (tppt) REVERT: G 34 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9067 (mp) REVERT: H 34 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9259 (mp) REVERT: I 28 LYS cc_start: 0.8690 (tttm) cc_final: 0.8332 (tppt) REVERT: I 34 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9125 (mp) REVERT: J 34 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9288 (mt) outliers start: 13 outliers final: 4 residues processed: 51 average time/residue: 0.0667 time to fit residues: 3.9040 Evaluate side-chains 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.0060 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.129409 restraints weight = 3829.130| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.65 r_work: 0.4262 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2060 Z= 0.103 Angle : 0.491 3.115 2760 Z= 0.268 Chirality : 0.050 0.121 330 Planarity : 0.001 0.009 340 Dihedral : 12.711 59.503 340 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.00 % Allowed : 33.50 % Favored : 60.50 % 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: -1.01 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 19 HIS 0.000 0.000 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 2060) covalent geometry : angle 0.49064 / 0.27 ( 2760) hydrogen bonds : bond 0.00916 / 0.68 ( 36) hydrogen bonds : angle 3.48779 / 2.28 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.058 Fit side-chains REVERT: A 34 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8900 (mt) REVERT: B 22 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: B 34 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9043 (mt) REVERT: C 34 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9139 (mp) REVERT: D 34 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9290 (mt) REVERT: E 34 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8928 (mp) REVERT: F 34 LEU cc_start: 0.9436 (mp) cc_final: 0.9064 (mt) REVERT: G 28 LYS cc_start: 0.8675 (tttm) cc_final: 0.8172 (tppt) REVERT: G 34 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8964 (mp) REVERT: H 34 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9348 (mp) REVERT: I 28 LYS cc_start: 0.8646 (tttm) cc_final: 0.8230 (tppt) REVERT: I 34 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8964 (mp) REVERT: I 40 VAL cc_start: 0.9182 (t) cc_final: 0.8849 (m) REVERT: J 34 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9248 (mt) outliers start: 12 outliers final: 2 residues processed: 57 average time/residue: 0.0593 time to fit residues: 3.8643 Evaluate side-chains 66 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.123882 restraints weight = 3931.796| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.69 r_work: 0.4172 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2060 Z= 0.203 Angle : 0.549 3.541 2760 Z= 0.295 Chirality : 0.050 0.123 330 Planarity : 0.001 0.009 340 Dihedral : 13.190 57.588 340 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.00 % Allowed : 34.00 % Favored : 60.00 % 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: -0.99 (0.49), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 19 HIS 0.000 0.000 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 2060) covalent geometry : angle 0.54932 / 0.30 ( 2760) hydrogen bonds : bond 0.01189 / 0.84 ( 36) hydrogen bonds : angle 3.40042 / 2.23 ( 108) =============================================================================== Job complete usr+sys time: 857.18 seconds wall clock time: 15 minutes 21.21 seconds (921.21 seconds total)