Starting phenix.real_space_refine on Wed Sep 17 03:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0e_61945/09_2025/9k0e_61945.map" } resolution = 2.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1230 2.51 5 N 330 2.21 5 O 324 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1890 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 234 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, N, H, O, I, A, L, D, M, E Time building chain proxies: 0.50, per 1000 atoms: 0.26 Number of scatterers: 1890 At special positions: 0 Unit cell: (66.4, 100.43, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 324 8.00 N 330 7.00 C 1230 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: 0.14 Conformation dependent library (CDL) restraints added in 78.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'N' and resid 31 through 33 removed outlier: 6.223A pdb=" N ILE G 31 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 39 through 41 removed outlier: 6.816A pdb=" N VAL G 40 " --> pdb=" O ILE N 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.377A pdb=" N VAL F 12 " --> pdb=" O HIS L 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 31 through 33 removed outlier: 6.248A pdb=" N ILE B 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.800A pdb=" N VAL B 40 " --> pdb=" O ILE H 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.420A pdb=" N VAL A 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) 14 hydrogen bonds defined for protein. 42 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: 0.22 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 612 1.34 - 1.45: 217 1.45 - 1.56: 1073 1.56 - 1.68: 0 1.68 - 1.79: 12 Bond restraints: 1914 Sorted by residual: bond pdb=" CB ILE I 32 " pdb=" CG2 ILE I 32 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.13e-01 bond pdb=" CB ILE B 32 " pdb=" CG2 ILE B 32 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.05e-01 bond pdb=" CA VAL G 36 " pdb=" CB VAL G 36 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.98e-01 bond pdb=" CB ILE O 32 " pdb=" CG2 ILE O 32 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.97e-01 bond pdb=" CB ILE G 32 " pdb=" CG2 ILE G 32 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.94e-01 ... (remaining 1909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 2211 0.79 - 1.57: 258 1.57 - 2.36: 63 2.36 - 3.15: 16 3.15 - 3.94: 14 Bond angle restraints: 2562 Sorted by residual: angle pdb=" N GLN N 15 " pdb=" CA GLN N 15 " pdb=" C GLN N 15 " ideal model delta sigma weight residual 107.93 111.10 -3.17 1.65e+00 3.67e-01 3.70e+00 angle pdb=" N GLN B 15 " pdb=" CA GLN B 15 " pdb=" C GLN B 15 " ideal model delta sigma weight residual 107.93 111.09 -3.16 1.65e+00 3.67e-01 3.66e+00 angle pdb=" N GLN G 15 " pdb=" CA GLN G 15 " pdb=" C GLN G 15 " ideal model delta sigma weight residual 107.93 111.07 -3.14 1.65e+00 3.67e-01 3.63e+00 angle pdb=" N GLN H 15 " pdb=" CA GLN H 15 " pdb=" C GLN H 15 " ideal model delta sigma weight residual 107.93 111.05 -3.12 1.65e+00 3.67e-01 3.57e+00 angle pdb=" N GLN O 15 " pdb=" CA GLN O 15 " pdb=" C GLN O 15 " ideal model delta sigma weight residual 107.93 111.04 -3.11 1.65e+00 3.67e-01 3.56e+00 ... (remaining 2557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.69: 858 10.69 - 21.38: 108 21.38 - 32.07: 42 32.07 - 42.76: 60 42.76 - 53.45: 12 Dihedral angle restraints: 1080 sinusoidal: 414 harmonic: 666 Sorted by residual: dihedral pdb=" CA LEU L 17 " pdb=" CB LEU L 17 " pdb=" CG LEU L 17 " pdb=" CD1 LEU L 17 " ideal model delta sinusoidal sigma weight residual 180.00 126.55 53.45 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA LEU F 17 " pdb=" CB LEU F 17 " pdb=" CG LEU F 17 " pdb=" CD1 LEU F 17 " ideal model delta sinusoidal sigma weight residual 180.00 126.56 53.44 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA LEU M 17 " pdb=" CB LEU M 17 " pdb=" CG LEU M 17 " pdb=" CD1 LEU M 17 " ideal model delta sinusoidal sigma weight residual 180.00 126.58 53.42 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 1077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 125 0.024 - 0.047: 72 0.047 - 0.071: 29 0.071 - 0.094: 26 0.094 - 0.118: 48 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL F 18 " pdb=" N VAL F 18 " pdb=" C VAL F 18 " pdb=" CB VAL F 18 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL A 18 " pdb=" N VAL A 18 " pdb=" C VAL A 18 " pdb=" CB VAL A 18 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 297 not shown) Planarity restraints: 318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 17 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C LEU G 17 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU G 17 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL G 18 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 17 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C LEU N 17 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU N 17 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL N 18 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 17 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C LEU O 17 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU O 17 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL O 18 " 0.008 2.00e-02 2.50e+03 ... (remaining 315 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 157 2.75 - 3.29: 1811 3.29 - 3.82: 3022 3.82 - 4.36: 3541 4.36 - 4.90: 6868 Nonbonded interactions: 15399 Sorted by model distance: nonbonded pdb=" NE2 GLN H 15 " pdb=" OE1 GLN D 15 " model vdw 2.209 3.120 nonbonded pdb=" NE2 GLN I 15 " pdb=" OE1 GLN E 15 " model vdw 2.209 3.120 nonbonded pdb=" NE2 GLN G 15 " pdb=" OE1 GLN F 15 " model vdw 2.210 3.120 nonbonded pdb=" NE2 GLN N 15 " pdb=" OE1 GLN L 15 " model vdw 2.210 3.120 nonbonded pdb=" NE2 GLN B 15 " pdb=" OE1 GLN A 15 " model vdw 2.210 3.120 ... (remaining 15394 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 'G' selection = chain 'B' selection = chain 'N' selection = chain 'H' selection = chain 'O' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'L' selection = chain 'D' selection = chain 'M' selection = chain 'E' } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.920 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:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.006 0.030 1914 Z= 0.273 Angle : 0.644 3.935 2562 Z= 0.374 Chirality : 0.056 0.118 300 Planarity : 0.003 0.014 318 Dihedral : 16.577 53.450 648 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % 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 aren not related in a simple way. whole: -3.39 (0.49), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 19 HIS 0.004 0.001 HIS M 13 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 1914) covalent geometry : angle 0.64420 ( 2562) hydrogen bonds : bond 0.28362 ( 14) hydrogen bonds : angle 10.78038 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.074 Fit side-chains REVERT: G 13 HIS cc_start: 0.6547 (m90) cc_final: 0.6254 (t70) REVERT: B 13 HIS cc_start: 0.6834 (m90) cc_final: 0.5970 (t70) REVERT: N 13 HIS cc_start: 0.7292 (m90) cc_final: 0.6427 (t70) REVERT: N 17 LEU cc_start: 0.9040 (tt) cc_final: 0.8802 (tt) REVERT: H 13 HIS cc_start: 0.7206 (m90) cc_final: 0.6369 (t70) REVERT: O 13 HIS cc_start: 0.6808 (m90) cc_final: 0.6428 (t70) REVERT: I 13 HIS cc_start: 0.6548 (m90) cc_final: 0.6313 (t70) outliers start: 0 outliers final: 1 residues processed: 36 average time/residue: 0.2558 time to fit residues: 9.5847 Evaluate side-chains 31 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS N 14 HIS H 14 HIS O 14 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.178385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.115825 restraints weight = 2198.752| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.99 r_work: 0.3591 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1914 Z= 0.182 Angle : 0.487 4.748 2562 Z= 0.270 Chirality : 0.056 0.120 300 Planarity : 0.002 0.015 318 Dihedral : 4.586 16.155 236 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % 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 aren not related in a simple way. whole: -2.58 (0.53), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE E 19 HIS 0.003 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 1914) covalent geometry : angle 0.48710 ( 2562) hydrogen bonds : bond 0.04097 ( 14) hydrogen bonds : angle 10.06272 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.052 Fit side-chains REVERT: G 13 HIS cc_start: 0.6397 (m90) cc_final: 0.5739 (t70) REVERT: B 13 HIS cc_start: 0.6722 (m90) cc_final: 0.5608 (t70) REVERT: N 13 HIS cc_start: 0.7400 (m90) cc_final: 0.6370 (t70) REVERT: N 17 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8792 (tt) REVERT: H 13 HIS cc_start: 0.7351 (m90) cc_final: 0.6338 (t70) REVERT: I 13 HIS cc_start: 0.6440 (m90) cc_final: 0.6045 (t70) outliers start: 3 outliers final: 0 residues processed: 37 average time/residue: 0.2483 time to fit residues: 9.5467 Evaluate side-chains 28 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS E 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.181154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.118224 restraints weight = 2216.583| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.05 r_work: 0.3654 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 1914 Z= 0.126 Angle : 0.415 3.879 2562 Z= 0.234 Chirality : 0.054 0.119 300 Planarity : 0.002 0.013 318 Dihedral : 3.989 10.412 234 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.52 % Allowed : 19.19 % Favored : 79.29 % 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 aren not related in a simple way. whole: -1.92 (0.55), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE H 19 HIS 0.005 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 1914) covalent geometry : angle 0.41544 ( 2562) hydrogen bonds : bond 0.03994 ( 14) hydrogen bonds : angle 9.54580 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.081 Fit side-chains REVERT: G 13 HIS cc_start: 0.6492 (m90) cc_final: 0.5730 (t70) REVERT: B 13 HIS cc_start: 0.6711 (m90) cc_final: 0.5456 (t-90) REVERT: N 13 HIS cc_start: 0.7380 (m90) cc_final: 0.6382 (t70) REVERT: N 17 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8770 (tt) REVERT: H 13 HIS cc_start: 0.7273 (m90) cc_final: 0.6315 (t70) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.2961 time to fit residues: 10.4428 Evaluate side-chains 26 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 17 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.174106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112172 restraints weight = 2206.610| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.03 r_work: 0.3576 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 1914 Z= 0.255 Angle : 0.520 3.767 2562 Z= 0.292 Chirality : 0.056 0.117 300 Planarity : 0.003 0.013 318 Dihedral : 4.539 10.725 234 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.02 % Favored : 81.98 % Rotamer: Outliers : 3.03 % Allowed : 20.20 % Favored : 76.77 % 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 aren not related in a simple way. whole: -1.95 (0.55), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE G 19 HIS 0.006 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 1914) covalent geometry : angle 0.52021 ( 2562) hydrogen bonds : bond 0.03827 ( 14) hydrogen bonds : angle 9.06038 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.084 Fit side-chains REVERT: G 13 HIS cc_start: 0.6518 (m90) cc_final: 0.5767 (t70) REVERT: B 13 HIS cc_start: 0.6770 (m90) cc_final: 0.5497 (t70) REVERT: B 17 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8399 (tt) REVERT: N 13 HIS cc_start: 0.7464 (m90) cc_final: 0.6367 (t70) REVERT: N 17 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8878 (tt) REVERT: H 13 HIS cc_start: 0.7264 (m90) cc_final: 0.6286 (t70) outliers start: 6 outliers final: 0 residues processed: 35 average time/residue: 0.2389 time to fit residues: 8.7588 Evaluate side-chains 33 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain N residue 17 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.178116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116527 restraints weight = 2181.638| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.02 r_work: 0.3629 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1914 Z= 0.160 Angle : 0.438 4.068 2562 Z= 0.248 Chirality : 0.054 0.119 300 Planarity : 0.002 0.014 318 Dihedral : 4.185 10.110 234 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.52 % Allowed : 24.24 % Favored : 74.24 % 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 aren not related in a simple way. whole: -1.70 (0.56), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE N 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 1914) covalent geometry : angle 0.43814 ( 2562) hydrogen bonds : bond 0.03698 ( 14) hydrogen bonds : angle 8.87804 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.094 Fit side-chains REVERT: B 13 HIS cc_start: 0.6789 (m90) cc_final: 0.5512 (t70) REVERT: B 17 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8399 (tt) REVERT: N 13 HIS cc_start: 0.7456 (m90) cc_final: 0.6377 (t70) REVERT: H 13 HIS cc_start: 0.7256 (m90) cc_final: 0.6285 (t70) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.2268 time to fit residues: 8.0907 Evaluate side-chains 28 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain O residue 13 HIS Chi-restraints excluded: chain O residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 HIS N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.182622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120860 restraints weight = 2167.008| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.98 r_work: 0.3687 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1914 Z= 0.100 Angle : 0.401 3.624 2562 Z= 0.228 Chirality : 0.053 0.122 300 Planarity : 0.002 0.012 318 Dihedral : 3.803 9.553 234 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.01 % Allowed : 26.77 % Favored : 72.22 % 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 aren not related in a simple way. whole: -1.33 (0.57), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 1914) covalent geometry : angle 0.40140 ( 2562) hydrogen bonds : bond 0.03488 ( 14) hydrogen bonds : angle 8.70202 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.077 Fit side-chains REVERT: G 13 HIS cc_start: 0.6474 (m90) cc_final: 0.5818 (t70) REVERT: B 13 HIS cc_start: 0.6767 (m90) cc_final: 0.5549 (t70) REVERT: N 13 HIS cc_start: 0.7379 (m90) cc_final: 0.6378 (t70) REVERT: H 13 HIS cc_start: 0.7108 (m90) cc_final: 0.6273 (t70) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.2747 time to fit residues: 9.7042 Evaluate side-chains 27 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.179705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118753 restraints weight = 2275.151| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.92 r_work: 0.3726 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1914 Z= 0.127 Angle : 0.415 3.990 2562 Z= 0.236 Chirality : 0.053 0.121 300 Planarity : 0.002 0.013 318 Dihedral : 3.862 9.421 234 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.02 % Allowed : 25.25 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.57), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE B 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 1914) covalent geometry : angle 0.41488 ( 2562) hydrogen bonds : bond 0.03491 ( 14) hydrogen bonds : angle 8.42075 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.085 Fit side-chains REVERT: G 13 HIS cc_start: 0.6449 (m90) cc_final: 0.5775 (t70) REVERT: B 13 HIS cc_start: 0.6805 (m90) cc_final: 0.5426 (t-90) REVERT: N 13 HIS cc_start: 0.7315 (m90) cc_final: 0.6328 (t70) REVERT: H 13 HIS cc_start: 0.6962 (m90) cc_final: 0.6174 (t-90) outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 0.2277 time to fit residues: 8.1098 Evaluate side-chains 27 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.179418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.118568 restraints weight = 2316.979| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.88 r_work: 0.3729 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1914 Z= 0.137 Angle : 0.436 4.314 2562 Z= 0.248 Chirality : 0.053 0.121 300 Planarity : 0.002 0.013 318 Dihedral : 3.924 9.357 234 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.52 % Allowed : 27.78 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.57), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE I 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 1914) covalent geometry : angle 0.43562 ( 2562) hydrogen bonds : bond 0.03463 ( 14) hydrogen bonds : angle 8.16419 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.087 Fit side-chains REVERT: G 13 HIS cc_start: 0.6465 (m90) cc_final: 0.5888 (t70) REVERT: B 13 HIS cc_start: 0.6858 (m90) cc_final: 0.5456 (t-90) REVERT: B 17 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8575 (tt) REVERT: N 13 HIS cc_start: 0.7283 (m90) cc_final: 0.6253 (t70) REVERT: H 13 HIS cc_start: 0.6930 (m90) cc_final: 0.6187 (t-90) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.2537 time to fit residues: 8.7520 Evaluate side-chains 30 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain O residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.181173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.119372 restraints weight = 2314.248| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.89 r_work: 0.3744 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1914 Z= 0.118 Angle : 0.422 4.175 2562 Z= 0.239 Chirality : 0.053 0.122 300 Planarity : 0.002 0.013 318 Dihedral : 3.811 9.194 234 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.52 % Allowed : 28.28 % Favored : 70.20 % 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 aren not related in a simple way. whole: -1.02 (0.57), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE N 19 HIS 0.006 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 1914) covalent geometry : angle 0.42153 ( 2562) hydrogen bonds : bond 0.03460 ( 14) hydrogen bonds : angle 8.13158 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.068 Fit side-chains REVERT: G 13 HIS cc_start: 0.6388 (m90) cc_final: 0.5891 (t70) REVERT: B 13 HIS cc_start: 0.6790 (m90) cc_final: 0.5452 (t-90) REVERT: N 13 HIS cc_start: 0.7320 (m90) cc_final: 0.6319 (t70) REVERT: H 13 HIS cc_start: 0.6931 (m90) cc_final: 0.6179 (t-90) outliers start: 3 outliers final: 0 residues processed: 32 average time/residue: 0.2676 time to fit residues: 8.8997 Evaluate side-chains 28 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS O 14 HIS I 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.184680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123230 restraints weight = 2276.920| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.87 r_work: 0.3802 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1914 Z= 0.103 Angle : 0.418 4.320 2562 Z= 0.237 Chirality : 0.053 0.122 300 Planarity : 0.002 0.014 318 Dihedral : 3.589 9.032 234 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.51 % Allowed : 29.29 % Favored : 70.20 % 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 aren not related in a simple way. whole: -0.80 (0.58), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE N 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 1914) covalent geometry : angle 0.41798 ( 2562) hydrogen bonds : bond 0.03527 ( 14) hydrogen bonds : angle 8.04669 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 444 Ramachandran restraints generated. 222 Oldfield, 0 Emsley, 222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.050 Fit side-chains REVERT: G 13 HIS cc_start: 0.6254 (m90) cc_final: 0.5770 (t70) REVERT: B 13 HIS cc_start: 0.6729 (m90) cc_final: 0.5446 (t-90) REVERT: N 13 HIS cc_start: 0.7227 (m90) cc_final: 0.6234 (t70) REVERT: H 13 HIS cc_start: 0.7103 (m90) cc_final: 0.6163 (t-90) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.2549 time to fit residues: 7.9910 Evaluate side-chains 27 residues out of total 198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 14 HIS H 14 HIS I 14 HIS E 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.181839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.121276 restraints weight = 2333.120| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.97 r_work: 0.3764 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1914 Z= 0.117 Angle : 0.454 6.403 2562 Z= 0.248 Chirality : 0.053 0.132 300 Planarity : 0.002 0.016 318 Dihedral : 3.643 9.052 234 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.01 % Allowed : 28.28 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.59), residues: 222 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE N 19 HIS 0.006 0.001 HIS M 14 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 1914) covalent geometry : angle 0.45430 ( 2562) hydrogen bonds : bond 0.03463 ( 14) hydrogen bonds : angle 7.86802 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 922.83 seconds wall clock time: 16 minutes 27.58 seconds (987.58 seconds total)