Starting phenix.real_space_refine on Tue Aug 4 12:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.map" model { file = "/net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oif_70522/08_2026/9oif_70522.cif" } resolution = 3.1 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= 0.001 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 20 5.16 5 C 1610 2.51 5 N 450 2.21 5 O 460 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2540 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 254 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.42, per 1000 atoms: 0.17 Number of scatterers: 2540 At special positions: 0 Unit cell: (71.514, 97.818, 40.278, 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 20 16.00 O 460 8.00 N 450 7.00 C 1610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 22 " distance=2.04 Simple disulfide: pdb=" SG CYS D 5 " - pdb=" SG CYS D 22 " distance=2.04 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 22 " distance=2.04 Simple disulfide: pdb=" SG CYS F 5 " - pdb=" SG CYS F 22 " distance=2.04 Simple disulfide: pdb=" SG CYS G 5 " - pdb=" SG CYS G 22 " distance=2.04 Simple disulfide: pdb=" SG CYS H 5 " - pdb=" SG CYS H 22 " distance=2.04 Simple disulfide: pdb=" SG CYS I 5 " - pdb=" SG CYS I 22 " distance=2.04 Simple disulfide: pdb=" SG CYS J 5 " - pdb=" SG CYS J 22 " distance=2.04 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: 0.13 Conformation dependent library (CDL) restraints added in 56.2 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 20.0% 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 'C' and resid 20 through 21 removed outlier: 6.229A pdb=" N LEU A 20 " --> pdb=" O ILE E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.923A pdb=" N LYS C 27 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS E 28 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N VAL A 26 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASN E 29 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS A 28 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE E 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS A 27 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS G 28 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS I 28 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 6.163A pdb=" N LEU F 20 " --> pdb=" O ILE J 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 31 removed outlier: 6.921A pdb=" N LYS B 27 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS D 28 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 27 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS J 28 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N LYS J 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N VAL F 26 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN J 29 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS F 28 " --> pdb=" O ASN J 29 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE J 31 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR F 25 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL H 26 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS F 27 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS H 28 " --> pdb=" O LYS F 27 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.33 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 830 1.35 - 1.47: 570 1.47 - 1.60: 1150 1.60 - 1.72: 0 1.72 - 1.84: 20 Bond restraints: 2570 Sorted by residual: bond pdb=" N SER F 3 " pdb=" CA SER F 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N SER I 3 " pdb=" CA SER I 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N SER J 3 " pdb=" CA SER J 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 ... (remaining 2565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 2825 1.48 - 2.96: 493 2.96 - 4.44: 100 4.44 - 5.92: 2 5.92 - 7.40: 10 Bond angle restraints: 3430 Sorted by residual: angle pdb=" N ALA E 7 " pdb=" CA ALA E 7 " pdb=" C ALA E 7 " ideal model delta sigma weight residual 108.63 116.03 -7.40 1.60e+00 3.91e-01 2.14e+01 angle pdb=" N ALA I 7 " pdb=" CA ALA I 7 " pdb=" C ALA I 7 " ideal model delta sigma weight residual 108.63 116.01 -7.38 1.60e+00 3.91e-01 2.13e+01 angle pdb=" N ALA H 7 " pdb=" CA ALA H 7 " pdb=" C ALA H 7 " ideal model delta sigma weight residual 108.63 116.00 -7.37 1.60e+00 3.91e-01 2.12e+01 angle pdb=" N ALA J 7 " pdb=" CA ALA J 7 " pdb=" C ALA J 7 " ideal model delta sigma weight residual 108.63 116.00 -7.37 1.60e+00 3.91e-01 2.12e+01 angle pdb=" N ALA F 7 " pdb=" CA ALA F 7 " pdb=" C ALA F 7 " ideal model delta sigma weight residual 108.63 115.99 -7.36 1.60e+00 3.91e-01 2.11e+01 ... (remaining 3425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 1320 13.93 - 27.85: 230 27.85 - 41.78: 40 41.78 - 55.71: 10 55.71 - 69.63: 10 Dihedral angle restraints: 1610 sinusoidal: 690 harmonic: 920 Sorted by residual: dihedral pdb=" CA PHE F 6 " pdb=" C PHE F 6 " pdb=" N ALA F 7 " pdb=" CA ALA F 7 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA PHE B 6 " pdb=" C PHE B 6 " pdb=" N ALA B 7 " pdb=" CA ALA B 7 " ideal model delta harmonic sigma weight residual -180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA PHE G 6 " pdb=" C PHE G 6 " pdb=" N ALA G 7 " pdb=" CA ALA G 7 " ideal model delta harmonic sigma weight residual 180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 185 0.036 - 0.071: 135 0.071 - 0.107: 0 0.107 - 0.143: 24 0.143 - 0.178: 56 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA PHE F 11 " pdb=" N PHE F 11 " pdb=" C PHE F 11 " pdb=" CB PHE F 11 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA PHE J 11 " pdb=" N PHE J 11 " pdb=" C PHE J 11 " pdb=" CB PHE J 11 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA PHE C 11 " pdb=" N PHE C 11 " pdb=" C PHE C 11 " pdb=" CB PHE C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 397 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 11 " -0.004 2.00e-02 2.50e+03 2.28e-02 9.08e+00 pdb=" CG PHE J 11 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE J 11 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE J 11 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE J 11 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE J 11 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE J 11 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 11 " -0.004 2.00e-02 2.50e+03 2.28e-02 9.07e+00 pdb=" CG PHE F 11 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE F 11 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE F 11 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE F 11 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE F 11 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 11 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 11 " 0.004 2.00e-02 2.50e+03 2.27e-02 9.05e+00 pdb=" CG PHE C 11 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 11 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE C 11 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 11 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE C 11 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 11 " 0.007 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 1513 3.09 - 3.54: 2308 3.54 - 3.99: 3668 3.99 - 4.45: 3994 4.45 - 4.90: 8100 Nonbonded interactions: 19583 Sorted by model distance: nonbonded pdb=" O ARG A 9 " pdb=" N HIS G 10 " model vdw 2.637 3.120 nonbonded pdb=" O LYS A 14 " pdb=" N PHE G 15 " model vdw 2.639 3.120 nonbonded pdb=" O VAL A 17 " pdb=" N GLU G 18 " model vdw 2.643 3.120 nonbonded pdb=" N GLU G 32 " pdb=" O GLU G 32 " model vdw 2.651 2.496 nonbonded pdb=" N GLU F 32 " pdb=" O GLU F 32 " model vdw 2.651 2.496 ... (remaining 19578 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.010 0.052 2580 Z= 0.425 Angle : 1.269 7.395 3450 Z= 0.771 Chirality : 0.074 0.178 400 Planarity : 0.007 0.023 430 Dihedral : 14.990 69.633 960 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.87 (0.28), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.21), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 9 PHE 0.038 0.009 PHE E 11 HIS 0.000 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00955 / 0.43 ( 2570) covalent geometry : angle 1.25230 / 0.77 ( 3430) SS BOND : bond 0.00602 / 0.40 ( 10) SS BOND : angle 2.93708 / 2.00 ( 20) hydrogen bonds : bond 0.18531 / 12.37 ( 24) hydrogen bonds : angle 12.24560 / 8.54 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.059 Fit side-chains REVERT: B 18 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6482 (mp0) REVERT: G 6 PHE cc_start: 0.6523 (m-10) cc_final: 0.6235 (m-10) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0514 time to fit residues: 2.7623 Evaluate side-chains 32 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4888 r_free = 0.4888 target = 0.148866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.122284 restraints weight = 2766.918| |-----------------------------------------------------------------------------| r_work (start): 0.4572 rms_B_bonded: 3.22 r_work: 0.4343 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2580 Z= 0.225 Angle : 1.050 13.278 3450 Z= 0.569 Chirality : 0.064 0.153 400 Planarity : 0.003 0.012 430 Dihedral : 10.468 28.765 320 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.97 % Favored : 81.03 % Rotamer: Outliers : 3.45 % Allowed : 8.97 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.74 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 24 PHE 0.014 0.002 PHE A 11 HIS 0.002 0.001 HIS F 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 ( 2570) covalent geometry : angle 0.98394 / 0.54 ( 3430) SS BOND : bond 0.00694 / 0.42 ( 10) SS BOND : angle 4.91097 / 2.98 ( 20) hydrogen bonds : bond 0.03905 / 2.60 ( 24) hydrogen bonds : angle 8.02305 / 5.85 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.057 Fit side-chains REVERT: C 18 GLU cc_start: 0.7758 (mp0) cc_final: 0.7487 (mp0) REVERT: H 3 SER cc_start: 0.6838 (m) cc_final: 0.6480 (t) REVERT: I 3 SER cc_start: 0.6634 (m) cc_final: 0.6405 (t) outliers start: 10 outliers final: 0 residues processed: 49 average time/residue: 0.0213 time to fit residues: 1.4992 Evaluate side-chains 30 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.169571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.140097 restraints weight = 2722.186| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.33 r_work: 0.4451 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2580 Z= 0.182 Angle : 0.958 12.608 3450 Z= 0.512 Chirality : 0.059 0.153 400 Planarity : 0.002 0.007 430 Dihedral : 9.750 28.342 320 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.21 % Favored : 83.79 % Rotamer: Outliers : 3.10 % Allowed : 14.14 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.52 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 24 PHE 0.010 0.001 PHE F 6 HIS 0.001 0.000 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 ( 2570) covalent geometry : angle 0.88239 / 0.48 ( 3430) SS BOND : bond 0.00806 / 0.55 ( 10) SS BOND : angle 4.97555 / 3.06 ( 20) hydrogen bonds : bond 0.02863 / 1.84 ( 24) hydrogen bonds : angle 7.23676 / 5.29 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.058 Fit side-chains REVERT: C 18 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: D 18 GLU cc_start: 0.6934 (mp0) cc_final: 0.6565 (mt-10) REVERT: E 33 GLU cc_start: 0.6326 (tt0) cc_final: 0.5876 (mt-10) REVERT: G 4 ASN cc_start: 0.7331 (m-40) cc_final: 0.6750 (m-40) REVERT: G 6 PHE cc_start: 0.6512 (m-10) cc_final: 0.6275 (t80) REVERT: J 4 ASN cc_start: 0.7286 (m110) cc_final: 0.7070 (m-40) outliers start: 9 outliers final: 1 residues processed: 41 average time/residue: 0.0227 time to fit residues: 1.2805 Evaluate side-chains 32 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4867 r_free = 0.4867 target = 0.148956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.122750 restraints weight = 2859.458| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 3.01 r_work: 0.4398 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2580 Z= 0.165 Angle : 0.840 11.389 3450 Z= 0.450 Chirality : 0.057 0.139 400 Planarity : 0.002 0.012 430 Dihedral : 9.167 28.726 320 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 3.79 % Allowed : 19.31 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.37 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 24 PHE 0.010 0.001 PHE I 6 HIS 0.001 0.000 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 2570) covalent geometry : angle 0.77432 / 0.42 ( 3430) SS BOND : bond 0.00450 / 0.29 ( 10) SS BOND : angle 4.33994 / 2.68 ( 20) hydrogen bonds : bond 0.02723 / 1.74 ( 24) hydrogen bonds : angle 6.95326 / 5.05 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.057 Fit side-chains REVERT: B 33 GLU cc_start: 0.5956 (tt0) cc_final: 0.5726 (mt-10) REVERT: C 18 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: E 33 GLU cc_start: 0.6012 (tt0) cc_final: 0.5539 (mt-10) REVERT: G 4 ASN cc_start: 0.7109 (m-40) cc_final: 0.6829 (m-40) REVERT: I 33 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6751 (mt-10) REVERT: J 4 ASN cc_start: 0.7153 (m110) cc_final: 0.6907 (m-40) REVERT: J 18 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7186 (mt-10) outliers start: 11 outliers final: 1 residues processed: 44 average time/residue: 0.0220 time to fit residues: 1.3340 Evaluate side-chains 35 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS C 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.121182 restraints weight = 2956.585| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.98 r_work: 0.4344 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2580 Z= 0.162 Angle : 0.786 10.215 3450 Z= 0.426 Chirality : 0.056 0.133 400 Planarity : 0.002 0.010 430 Dihedral : 8.917 28.601 320 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 5.52 % Allowed : 18.28 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 9 PHE 0.007 0.001 PHE E 11 HIS 0.001 0.000 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 2570) covalent geometry : angle 0.73516 / 0.40 ( 3430) SS BOND : bond 0.00382 / 0.24 ( 10) SS BOND : angle 3.74241 / 2.29 ( 20) hydrogen bonds : bond 0.02822 / 1.84 ( 24) hydrogen bonds : angle 6.97818 / 5.03 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.061 Fit side-chains REVERT: B 20 LEU cc_start: 0.8391 (mt) cc_final: 0.8184 (tp) REVERT: C 20 LEU cc_start: 0.8446 (mt) cc_final: 0.8102 (tp) REVERT: D 33 GLU cc_start: 0.6325 (tt0) cc_final: 0.5899 (mt-10) REVERT: E 33 GLU cc_start: 0.6165 (tt0) cc_final: 0.5686 (mt-10) REVERT: F 4 ASN cc_start: 0.6500 (m-40) cc_final: 0.6207 (m-40) REVERT: G 6 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5634 (m-80) REVERT: J 6 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.5590 (m-80) outliers start: 16 outliers final: 6 residues processed: 50 average time/residue: 0.0224 time to fit residues: 1.5248 Evaluate side-chains 43 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain F residue 10 HIS Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 HIS D 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.161290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.131651 restraints weight = 2598.895| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 3.19 r_work: 0.4309 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 2580 Z= 0.259 Angle : 0.889 10.502 3450 Z= 0.489 Chirality : 0.061 0.151 400 Planarity : 0.003 0.017 430 Dihedral : 9.474 31.115 320 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 6.55 % Allowed : 16.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.44 (0.31), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.24), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 9 PHE 0.011 0.002 PHE B 11 HIS 0.003 0.001 HIS H 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 ( 2570) covalent geometry : angle 0.82822 / 0.47 ( 3430) SS BOND : bond 0.00366 / 0.23 ( 10) SS BOND : angle 4.31621 / 2.74 ( 20) hydrogen bonds : bond 0.03658 / 2.38 ( 24) hydrogen bonds : angle 7.66988 / 5.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.065 Fit side-chains REVERT: A 33 GLU cc_start: 0.6614 (mp0) cc_final: 0.6373 (tm-30) REVERT: E 33 GLU cc_start: 0.6304 (tt0) cc_final: 0.5878 (mt-10) REVERT: J 6 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 19 outliers final: 9 residues processed: 52 average time/residue: 0.0268 time to fit residues: 1.8683 Evaluate side-chains 43 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain E residue 10 HIS Chi-restraints excluded: chain F residue 10 HIS Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.123726 restraints weight = 2668.602| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.22 r_work: 0.4368 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2580 Z= 0.195 Angle : 0.857 10.489 3450 Z= 0.459 Chirality : 0.058 0.138 400 Planarity : 0.003 0.019 430 Dihedral : 9.172 30.116 320 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 5.52 % Allowed : 17.93 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.33), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.25), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 9 PHE 0.009 0.001 PHE E 11 HIS 0.003 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 ( 2570) covalent geometry : angle 0.80466 / 0.44 ( 3430) SS BOND : bond 0.00432 / 0.28 ( 10) SS BOND : angle 3.97176 / 2.43 ( 20) hydrogen bonds : bond 0.03118 / 2.04 ( 24) hydrogen bonds : angle 7.39561 / 5.30 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.056 Fit side-chains REVERT: A 18 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7132 (mt-10) REVERT: A 33 GLU cc_start: 0.6406 (mp0) cc_final: 0.6196 (tm-30) REVERT: E 33 GLU cc_start: 0.6210 (tt0) cc_final: 0.5723 (mt-10) REVERT: F 32 GLU cc_start: 0.7384 (pt0) cc_final: 0.6690 (tt0) REVERT: G 6 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: G 33 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6482 (mt-10) REVERT: J 6 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: J 32 GLU cc_start: 0.7325 (pt0) cc_final: 0.6757 (tm-30) REVERT: J 33 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6740 (tm-30) outliers start: 16 outliers final: 8 residues processed: 47 average time/residue: 0.0236 time to fit residues: 1.4978 Evaluate side-chains 41 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain E residue 10 HIS Chi-restraints excluded: chain F residue 10 HIS Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.167017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.137448 restraints weight = 2597.763| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 3.33 r_work: 0.4390 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2580 Z= 0.181 Angle : 0.825 9.930 3450 Z= 0.441 Chirality : 0.057 0.134 400 Planarity : 0.003 0.015 430 Dihedral : 9.059 29.618 320 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 4.83 % Allowed : 19.66 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.33), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.25), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 9 PHE 0.008 0.001 PHE E 11 HIS 0.002 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 ( 2570) covalent geometry : angle 0.77922 / 0.42 ( 3430) SS BOND : bond 0.00379 / 0.24 ( 10) SS BOND : angle 3.64597 / 2.23 ( 20) hydrogen bonds : bond 0.03100 / 2.03 ( 24) hydrogen bonds : angle 7.08760 / 5.10 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.060 Fit side-chains REVERT: A 18 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7109 (mt-10) REVERT: A 33 GLU cc_start: 0.6373 (mp0) cc_final: 0.6160 (tm-30) REVERT: E 33 GLU cc_start: 0.6175 (tt0) cc_final: 0.5687 (mt-10) REVERT: F 32 GLU cc_start: 0.7290 (pt0) cc_final: 0.6607 (tt0) REVERT: G 6 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: J 6 PHE cc_start: 0.6249 (OUTLIER) cc_final: 0.5792 (m-80) REVERT: J 32 GLU cc_start: 0.7274 (pt0) cc_final: 0.6748 (tm-30) REVERT: J 33 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6815 (tm-30) outliers start: 14 outliers final: 8 residues processed: 43 average time/residue: 0.0251 time to fit residues: 1.4430 Evaluate side-chains 39 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain E residue 10 HIS Chi-restraints excluded: chain F residue 10 HIS Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 HIS F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.148702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.120140 restraints weight = 2779.350| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 3.22 r_work: 0.4206 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 2580 Z= 0.274 Angle : 0.921 10.130 3450 Z= 0.500 Chirality : 0.061 0.157 400 Planarity : 0.003 0.014 430 Dihedral : 9.383 31.281 320 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 5.52 % Allowed : 20.00 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.34), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 9 PHE 0.011 0.002 PHE D 11 HIS 0.004 0.001 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.27 ( 2570) covalent geometry : angle 0.86636 / 0.48 ( 3430) SS BOND : bond 0.00342 / 0.22 ( 10) SS BOND : angle 4.19446 / 2.66 ( 20) hydrogen bonds : bond 0.03951 / 2.57 ( 24) hydrogen bonds : angle 7.46440 / 5.42 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.058 Fit side-chains REVERT: E 33 GLU cc_start: 0.6239 (tt0) cc_final: 0.5795 (mt-10) REVERT: F 32 GLU cc_start: 0.7452 (pt0) cc_final: 0.6787 (tt0) REVERT: I 6 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: J 6 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: J 32 GLU cc_start: 0.7395 (pt0) cc_final: 0.6876 (tm-30) REVERT: J 33 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6949 (tm-30) outliers start: 16 outliers final: 9 residues processed: 48 average time/residue: 0.0377 time to fit residues: 2.2856 Evaluate side-chains 43 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain D residue 10 HIS Chi-restraints excluded: chain E residue 10 HIS Chi-restraints excluded: chain F residue 10 HIS Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.5124 r_free = 0.5124 target = 0.168672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.139166 restraints weight = 2669.970| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 3.38 r_work: 0.4451 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2580 Z= 0.156 Angle : 0.799 9.737 3450 Z= 0.428 Chirality : 0.056 0.155 400 Planarity : 0.004 0.029 430 Dihedral : 8.755 29.185 320 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.48 % Allowed : 20.69 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.34), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.26), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 9 PHE 0.008 0.001 PHE J 6 HIS 0.003 0.001 HIS J 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 2570) covalent geometry : angle 0.76322 / 0.41 ( 3430) SS BOND : bond 0.00534 / 0.35 ( 10) SS BOND : angle 3.19094 / 1.96 ( 20) hydrogen bonds : bond 0.02779 / 1.83 ( 24) hydrogen bonds : angle 6.85768 / 4.93 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.060 Fit side-chains REVERT: A 18 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7121 (mt-10) REVERT: A 33 GLU cc_start: 0.6939 (tm-30) cc_final: 0.5924 (mp0) REVERT: B 33 GLU cc_start: 0.6449 (tt0) cc_final: 0.5985 (mt-10) REVERT: C 6 PHE cc_start: 0.6706 (m-80) cc_final: 0.6496 (t80) REVERT: E 33 GLU cc_start: 0.5959 (tt0) cc_final: 0.5532 (mt-10) REVERT: F 6 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: F 32 GLU cc_start: 0.7243 (pt0) cc_final: 0.6550 (tt0) REVERT: G 6 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: I 6 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: J 6 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5749 (m-80) REVERT: J 32 GLU cc_start: 0.7242 (pt0) cc_final: 0.6698 (tm-30) REVERT: J 33 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6804 (tm-30) outliers start: 13 outliers final: 7 residues processed: 40 average time/residue: 0.0337 time to fit residues: 1.7379 Evaluate side-chains 38 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 HIS Chi-restraints excluded: chain C residue 10 HIS Chi-restraints excluded: chain E residue 10 HIS Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 10 HIS Chi-restraints excluded: chain H residue 10 HIS Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 10 HIS Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 10 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 10 HIS G 10 HIS H 10 HIS I 10 HIS J 10 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.166806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.137893 restraints weight = 2649.518| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.24 r_work: 0.4410 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.6531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2580 Z= 0.177 Angle : 0.791 9.003 3450 Z= 0.427 Chirality : 0.056 0.134 400 Planarity : 0.002 0.012 430 Dihedral : 8.613 29.885 320 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.48 % Allowed : 22.07 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.35), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.27), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 9 PHE 0.009 0.001 PHE C 11 HIS 0.002 0.000 HIS B 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 2570) covalent geometry : angle 0.75577 / 0.41 ( 3430) SS BOND : bond 0.00406 / 0.26 ( 10) SS BOND : angle 3.15676 / 1.98 ( 20) hydrogen bonds : bond 0.02921 / 1.91 ( 24) hydrogen bonds : angle 6.86088 / 4.98 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 665.78 seconds wall clock time: 12 minutes 2.17 seconds (722.17 seconds total)