Starting phenix.real_space_refine on Tue Feb 3 14:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.map" model { file = "/net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v91_64858/02_2026/9v91_64858.cif" } resolution = 3.0 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 12 5.16 5 C 2202 2.51 5 N 636 2.21 5 O 738 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.62, per 1000 atoms: 0.17 Number of scatterers: 3588 At special positions: 0 Unit cell: (154.38, 85.56, 35.34, 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 12 16.00 O 738 8.00 N 636 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 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: 0.28 Conformation dependent library (CDL) restraints added in 159.9 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.060A pdb=" N THR A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR B 19 " --> pdb=" O ILE C 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.060A pdb=" N THR D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR E 19 " --> pdb=" O ILE F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA9, first strand: chain 'D' and resid 76 through 77 Processing sheet with id=AB1, first strand: chain 'E' and resid 70 through 71 18 hydrogen bonds defined for protein. 54 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: 0.43 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1212 1.34 - 1.46: 832 1.46 - 1.58: 1616 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3672 Sorted by residual: bond pdb=" CB ASP E 83 " pdb=" CG ASP E 83 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.85e-01 bond pdb=" CB ASP F 83 " pdb=" CG ASP F 83 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.50e-01 bond pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.48e-01 bond pdb=" CB ASP B 83 " pdb=" CG ASP B 83 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.47e-01 bond pdb=" CB ASP D 83 " pdb=" CG ASP D 83 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.38e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4483 1.08 - 2.17: 397 2.17 - 3.25: 66 3.25 - 4.33: 34 4.33 - 5.41: 18 Bond angle restraints: 4998 Sorted by residual: angle pdb=" N ASP D 83 " pdb=" CA ASP D 83 " pdb=" C ASP D 83 " ideal model delta sigma weight residual 110.44 105.97 4.47 1.20e+00 6.94e-01 1.39e+01 angle pdb=" N ASP A 83 " pdb=" CA ASP A 83 " pdb=" C ASP A 83 " ideal model delta sigma weight residual 110.44 105.98 4.46 1.20e+00 6.94e-01 1.38e+01 angle pdb=" N ASP E 83 " pdb=" CA ASP E 83 " pdb=" C ASP E 83 " ideal model delta sigma weight residual 110.44 106.01 4.43 1.20e+00 6.94e-01 1.36e+01 angle pdb=" N ASP F 83 " pdb=" CA ASP F 83 " pdb=" C ASP F 83 " ideal model delta sigma weight residual 110.44 106.03 4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" N ASP C 83 " pdb=" CA ASP C 83 " pdb=" C ASP C 83 " ideal model delta sigma weight residual 110.44 106.04 4.40 1.20e+00 6.94e-01 1.34e+01 ... (remaining 4993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.99: 1644 10.99 - 21.98: 264 21.98 - 32.97: 162 32.97 - 43.96: 66 43.96 - 54.95: 36 Dihedral angle restraints: 2172 sinusoidal: 804 harmonic: 1368 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.62 37.62 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.57 37.57 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual -86.00 -123.57 37.57 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 2169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 294 0.030 - 0.059: 159 0.059 - 0.088: 56 0.088 - 0.118: 25 0.118 - 0.147: 6 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA TRP D 36 " pdb=" N TRP D 36 " pdb=" C TRP D 36 " pdb=" CB TRP D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA TRP A 36 " pdb=" N TRP A 36 " pdb=" C TRP A 36 " pdb=" CB TRP A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA TRP B 36 " pdb=" N TRP B 36 " pdb=" C TRP B 36 " pdb=" CB TRP B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 537 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 83 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ASP B 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP B 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 84 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 83 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C ASP E 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP E 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU E 84 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 83 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASP F 83 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP F 83 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU F 84 " 0.011 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 760 2.78 - 3.31: 3555 3.31 - 3.84: 5819 3.84 - 4.37: 6533 4.37 - 4.90: 12900 Nonbonded interactions: 29567 Sorted by model distance: nonbonded pdb=" O GLY D 30 " pdb=" ND2 ASN E 32 " model vdw 2.249 3.120 nonbonded pdb=" O GLY A 30 " pdb=" ND2 ASN B 32 " model vdw 2.249 3.120 nonbonded pdb=" O GLY E 30 " pdb=" ND2 ASN F 32 " model vdw 2.329 3.120 nonbonded pdb=" O GLY B 30 " pdb=" ND2 ASN C 32 " model vdw 2.329 3.120 nonbonded pdb=" ND2 ASN B 53 " pdb=" O ASN C 52 " model vdw 2.347 3.120 ... (remaining 29562 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' } 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: 4.080 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.080 Find NCS groups from input model: 0.030 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 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 : 0.003 0.021 3678 Z= 0.151 Angle : 0.747 5.414 5010 Z= 0.427 Chirality : 0.044 0.147 540 Planarity : 0.005 0.036 660 Dihedral : 17.026 54.952 1278 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.92 % Favored : 73.08 % Rotamer: Outliers : 0.00 % Allowed : 31.82 % Favored : 68.18 % 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: -5.84 (0.26), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.20), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 62 TYR 0.006 0.001 TYR E 50 PHE 0.020 0.003 PHE E 37 TRP 0.001 0.001 TRP F 92 HIS 0.003 0.001 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3672) covalent geometry : angle 0.74804 ( 4998) SS BOND : bond 0.00069 ( 6) SS BOND : angle 0.35189 ( 12) hydrogen bonds : bond 0.26004 ( 18) hydrogen bonds : angle 10.64570 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.125 Fit side-chains REVERT: A 38 GLN cc_start: 0.8283 (pm20) cc_final: 0.5493 (mm-40) REVERT: B 29 ILE cc_start: 0.6791 (mm) cc_final: 0.6399 (mm) REVERT: C 29 ILE cc_start: 0.7100 (mm) cc_final: 0.6796 (mm) REVERT: D 17 ARG cc_start: 0.5971 (ptm160) cc_final: 0.5593 (tpm170) REVERT: E 47 LEU cc_start: 0.7024 (pt) cc_final: 0.6824 (pp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2172 time to fit residues: 11.7073 Evaluate side-chains 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 39 HIS E 39 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN F 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.159735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.145901 restraints weight = 5227.454| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.32 r_work: 0.4102 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 3678 Z= 0.369 Angle : 1.142 7.862 5010 Z= 0.633 Chirality : 0.062 0.189 540 Planarity : 0.009 0.055 660 Dihedral : 9.242 28.858 510 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.64 % Allowed : 34.19 % Favored : 65.17 % Rotamer: Outliers : 9.85 % Allowed : 28.28 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.42 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.88 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 62 TYR 0.017 0.004 TYR F 87 PHE 0.039 0.008 PHE A 37 TRP 0.033 0.007 TRP E 92 HIS 0.008 0.002 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00800 ( 3672) covalent geometry : angle 1.14229 ( 4998) SS BOND : bond 0.01123 ( 6) SS BOND : angle 1.18212 ( 12) hydrogen bonds : bond 0.05210 ( 18) hydrogen bonds : angle 6.69618 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 48 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.5799 (t80) REVERT: A 93 ASP cc_start: 0.6173 (t70) cc_final: 0.5837 (t0) REVERT: B 29 ILE cc_start: 0.7688 (mm) cc_final: 0.7311 (mt) REVERT: B 39 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7576 (m170) REVERT: B 61 ASP cc_start: 0.5733 (OUTLIER) cc_final: 0.5447 (m-30) REVERT: B 74 LEU cc_start: 0.8056 (tt) cc_final: 0.7806 (tt) REVERT: C 29 ILE cc_start: 0.7934 (mm) cc_final: 0.7646 (mm) REVERT: C 35 ASN cc_start: 0.8462 (m110) cc_final: 0.8204 (m110) REVERT: C 39 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7839 (m170) REVERT: C 83 ASP cc_start: 0.7812 (t0) cc_final: 0.7562 (t0) REVERT: D 17 ARG cc_start: 0.7161 (ptm160) cc_final: 0.5936 (tpm170) REVERT: D 47 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8089 (pt) REVERT: D 61 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6269 (t0) REVERT: D 83 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7979 (t0) REVERT: E 61 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6477 (t0) REVERT: E 87 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7269 (t80) REVERT: F 87 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6696 (t80) outliers start: 39 outliers final: 11 residues processed: 83 average time/residue: 0.2654 time to fit residues: 23.4407 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 87 TYR Chi-restraints excluded: chain F residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN F 16 GLN F 32 ASN F 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.172211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.159243 restraints weight = 4955.688| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.22 r_work: 0.4297 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3678 Z= 0.166 Angle : 0.851 5.362 5010 Z= 0.460 Chirality : 0.047 0.142 540 Planarity : 0.007 0.050 660 Dihedral : 7.860 27.656 510 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 31.20 % Favored : 68.59 % Rotamer: Outliers : 6.82 % Allowed : 30.81 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.28 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.78 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.014 0.002 TYR B 50 PHE 0.020 0.003 PHE B 37 TRP 0.015 0.002 TRP F 92 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3672) covalent geometry : angle 0.85160 ( 4998) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.54217 ( 12) hydrogen bonds : bond 0.03312 ( 18) hydrogen bonds : angle 6.04578 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7188 (ptm160) cc_final: 0.6523 (tpp-160) REVERT: A 93 ASP cc_start: 0.6085 (t70) cc_final: 0.5784 (t0) REVERT: B 29 ILE cc_start: 0.7502 (mm) cc_final: 0.6961 (mm) REVERT: B 53 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: D 17 ARG cc_start: 0.6967 (ptm160) cc_final: 0.5844 (tpm170) REVERT: D 83 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (t0) REVERT: E 83 ASP cc_start: 0.7815 (t0) cc_final: 0.7613 (t0) REVERT: E 93 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7888 (m-30) outliers start: 27 outliers final: 9 residues processed: 61 average time/residue: 0.2824 time to fit residues: 18.2671 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.159498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.146427 restraints weight = 5162.051| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.12 r_work: 0.4140 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3678 Z= 0.287 Angle : 1.030 6.716 5010 Z= 0.570 Chirality : 0.055 0.152 540 Planarity : 0.008 0.066 660 Dihedral : 8.798 28.655 510 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 1.07 % Allowed : 36.54 % Favored : 62.39 % Rotamer: Outliers : 11.36 % Allowed : 32.58 % Favored : 56.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.44 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.014 0.003 TYR F 88 PHE 0.035 0.007 PHE A 37 TRP 0.027 0.005 TRP E 92 HIS 0.003 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 3672) covalent geometry : angle 1.03037 ( 4998) SS BOND : bond 0.00802 ( 6) SS BOND : angle 0.87205 ( 12) hydrogen bonds : bond 0.03653 ( 18) hydrogen bonds : angle 6.70537 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 46 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7235 (ptm160) cc_final: 0.6684 (tpp-160) REVERT: A 32 ASN cc_start: 0.8167 (m-40) cc_final: 0.7868 (m-40) REVERT: A 55 ARG cc_start: 0.7496 (ptp90) cc_final: 0.5932 (tpm170) REVERT: A 87 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.5421 (t80) REVERT: A 93 ASP cc_start: 0.6155 (t70) cc_final: 0.5833 (t0) REVERT: B 29 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7122 (mm) REVERT: B 79 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7537 (mt) REVERT: B 87 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.6309 (t80) REVERT: C 37 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.5809 (p90) REVERT: D 16 GLN cc_start: 0.6431 (pt0) cc_final: 0.6004 (pp30) REVERT: D 17 ARG cc_start: 0.7087 (ptm160) cc_final: 0.5798 (tpm170) REVERT: D 46 LYS cc_start: 0.8075 (mtmm) cc_final: 0.7494 (ttmt) REVERT: D 83 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7971 (t0) REVERT: E 93 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: F 37 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7594 (p90) outliers start: 45 outliers final: 18 residues processed: 81 average time/residue: 0.2662 time to fit residues: 22.8638 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain F residue 37 PHE Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 35 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS F 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.150079 restraints weight = 5169.260| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.16 r_work: 0.4192 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3678 Z= 0.223 Angle : 0.946 6.026 5010 Z= 0.519 Chirality : 0.052 0.148 540 Planarity : 0.008 0.076 660 Dihedral : 8.535 29.784 510 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 1.07 % Allowed : 32.48 % Favored : 66.45 % Rotamer: Outliers : 12.12 % Allowed : 30.81 % Favored : 57.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.37 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.17), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.013 0.002 TYR D 88 PHE 0.028 0.005 PHE A 37 TRP 0.022 0.004 TRP E 92 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 3672) covalent geometry : angle 0.94641 ( 4998) SS BOND : bond 0.00452 ( 6) SS BOND : angle 0.78282 ( 12) hydrogen bonds : bond 0.03005 ( 18) hydrogen bonds : angle 6.68037 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 39 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7280 (ptm160) cc_final: 0.6718 (tpp-160) REVERT: A 32 ASN cc_start: 0.8205 (m-40) cc_final: 0.7911 (m-40) REVERT: A 93 ASP cc_start: 0.6067 (t70) cc_final: 0.5772 (t0) REVERT: B 29 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7108 (mm) REVERT: C 39 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7317 (m170) REVERT: D 17 ARG cc_start: 0.6974 (ptm160) cc_final: 0.5809 (tpm170) REVERT: D 46 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7530 (ttmm) REVERT: D 83 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7890 (t0) REVERT: E 87 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.7018 (t80) outliers start: 48 outliers final: 18 residues processed: 78 average time/residue: 0.2324 time to fit residues: 19.4161 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 39 HIS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.178169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.165543 restraints weight = 4913.210| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.23 r_work: 0.4324 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4237 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3678 Z= 0.140 Angle : 0.782 4.912 5010 Z= 0.420 Chirality : 0.045 0.133 540 Planarity : 0.007 0.067 660 Dihedral : 7.325 27.009 510 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.64 % Allowed : 28.85 % Favored : 70.51 % Rotamer: Outliers : 7.07 % Allowed : 34.09 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.14 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 55 TYR 0.011 0.001 TYR B 50 PHE 0.014 0.002 PHE B 37 TRP 0.009 0.001 TRP F 92 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3672) covalent geometry : angle 0.78273 ( 4998) SS BOND : bond 0.00037 ( 6) SS BOND : angle 0.57109 ( 12) hydrogen bonds : bond 0.02236 ( 18) hydrogen bonds : angle 5.87489 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 33 time to evaluate : 0.133 Fit side-chains REVERT: A 17 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6732 (tpp-160) REVERT: A 38 GLN cc_start: 0.7694 (pm20) cc_final: 0.4477 (mm-40) REVERT: A 93 ASP cc_start: 0.5970 (t70) cc_final: 0.5668 (t0) REVERT: B 29 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6962 (mm) REVERT: D 17 ARG cc_start: 0.6988 (ptm160) cc_final: 0.5893 (tpm170) REVERT: D 83 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7809 (m-30) outliers start: 28 outliers final: 9 residues processed: 56 average time/residue: 0.2644 time to fit residues: 15.7796 Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 53 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN D 52 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.161176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.148228 restraints weight = 5193.884| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.21 r_work: 0.4192 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3678 Z= 0.260 Angle : 0.999 9.105 5010 Z= 0.547 Chirality : 0.053 0.149 540 Planarity : 0.008 0.073 660 Dihedral : 8.501 29.707 510 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.85 % Allowed : 35.26 % Favored : 63.89 % Rotamer: Outliers : 10.61 % Allowed : 31.06 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.35 (0.23), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.83 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.013 0.003 TYR F 88 PHE 0.034 0.006 PHE B 37 TRP 0.024 0.005 TRP F 92 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 3672) covalent geometry : angle 0.99964 ( 4998) SS BOND : bond 0.00663 ( 6) SS BOND : angle 0.85858 ( 12) hydrogen bonds : bond 0.02902 ( 18) hydrogen bonds : angle 6.53529 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 38 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7243 (ptm160) cc_final: 0.6757 (tpp-160) REVERT: A 32 ASN cc_start: 0.8266 (m-40) cc_final: 0.8054 (m-40) REVERT: A 87 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.5439 (t80) REVERT: A 93 ASP cc_start: 0.6171 (t70) cc_final: 0.5879 (t0) REVERT: B 29 ILE cc_start: 0.7665 (mm) cc_final: 0.7140 (mm) REVERT: B 37 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6378 (p90) REVERT: B 79 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7508 (mt) REVERT: C 17 ARG cc_start: 0.7504 (ptm160) cc_final: 0.6918 (ppt90) REVERT: C 37 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5632 (p90) REVERT: D 17 ARG cc_start: 0.7220 (ptm160) cc_final: 0.6136 (tpm170) REVERT: D 46 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7593 (ttmm) REVERT: D 83 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7882 (t0) outliers start: 42 outliers final: 16 residues processed: 75 average time/residue: 0.1860 time to fit residues: 14.7546 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 37 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.173078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.160692 restraints weight = 5078.564| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.15 r_work: 0.4324 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4230 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3678 Z= 0.154 Angle : 0.832 8.217 5010 Z= 0.446 Chirality : 0.046 0.136 540 Planarity : 0.007 0.067 660 Dihedral : 7.578 28.131 510 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 30.34 % Favored : 69.02 % Rotamer: Outliers : 6.06 % Allowed : 35.10 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.17 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.009 0.002 TYR B 50 PHE 0.018 0.003 PHE B 37 TRP 0.011 0.002 TRP F 92 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3672) covalent geometry : angle 0.83264 ( 4998) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.61579 ( 12) hydrogen bonds : bond 0.02260 ( 18) hydrogen bonds : angle 5.94272 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7221 (ptm160) cc_final: 0.6734 (tpp-160) REVERT: A 29 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 93 ASP cc_start: 0.6102 (t70) cc_final: 0.5841 (t0) REVERT: B 29 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7062 (mm) REVERT: B 32 ASN cc_start: 0.8936 (m-40) cc_final: 0.8713 (m110) REVERT: C 17 ARG cc_start: 0.7328 (ptm160) cc_final: 0.6904 (ppt90) REVERT: D 17 ARG cc_start: 0.7064 (ptm160) cc_final: 0.5976 (tpm170) REVERT: D 83 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: D 84 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7519 (mt-10) outliers start: 24 outliers final: 11 residues processed: 52 average time/residue: 0.2186 time to fit residues: 12.2021 Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 84 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN D 52 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.170060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.157553 restraints weight = 5009.516| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.18 r_work: 0.4300 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3678 Z= 0.172 Angle : 0.865 7.915 5010 Z= 0.465 Chirality : 0.047 0.136 540 Planarity : 0.008 0.068 660 Dihedral : 7.679 28.658 510 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 32.05 % Favored : 67.31 % Rotamer: Outliers : 6.06 % Allowed : 34.60 % Favored : 59.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.18 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 55 TYR 0.009 0.002 TYR F 88 PHE 0.022 0.004 PHE B 37 TRP 0.014 0.002 TRP F 92 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3672) covalent geometry : angle 0.86507 ( 4998) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.69628 ( 12) hydrogen bonds : bond 0.02360 ( 18) hydrogen bonds : angle 6.04762 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7257 (ptm160) cc_final: 0.6682 (tpp-160) REVERT: A 79 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 93 ASP cc_start: 0.6045 (t70) cc_final: 0.5756 (t0) REVERT: B 29 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7127 (mm) REVERT: C 17 ARG cc_start: 0.7414 (ptm160) cc_final: 0.6904 (ppt90) REVERT: D 17 ARG cc_start: 0.7093 (ptm160) cc_final: 0.5970 (tpm170) REVERT: D 83 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7816 (m-30) outliers start: 24 outliers final: 13 residues processed: 51 average time/residue: 0.3136 time to fit residues: 16.8759 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.174701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.162428 restraints weight = 5042.197| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.12 r_work: 0.4359 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4269 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3678 Z= 0.153 Angle : 0.829 7.858 5010 Z= 0.444 Chirality : 0.046 0.138 540 Planarity : 0.008 0.067 660 Dihedral : 7.444 28.116 510 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 29.70 % Favored : 70.09 % Rotamer: Outliers : 5.05 % Allowed : 35.86 % Favored : 59.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.10 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.19), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.009 0.002 TYR E 50 PHE 0.018 0.003 PHE B 37 TRP 0.012 0.002 TRP F 92 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3672) covalent geometry : angle 0.82987 ( 4998) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.65746 ( 12) hydrogen bonds : bond 0.02196 ( 18) hydrogen bonds : angle 5.83459 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6747 (tpp-160) REVERT: A 93 ASP cc_start: 0.6012 (t70) cc_final: 0.5736 (t0) REVERT: B 29 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7135 (mm) REVERT: C 17 ARG cc_start: 0.7329 (ptm160) cc_final: 0.6866 (ppt90) REVERT: D 17 ARG cc_start: 0.7093 (ptm160) cc_final: 0.5963 (tpm170) REVERT: D 83 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: F 83 ASP cc_start: 0.7552 (t0) cc_final: 0.7323 (t70) outliers start: 20 outliers final: 12 residues processed: 50 average time/residue: 0.2692 time to fit residues: 14.3363 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN E 39 HIS F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.170316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.158056 restraints weight = 4969.231| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.15 r_work: 0.4307 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4216 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3678 Z= 0.181 Angle : 0.880 7.493 5010 Z= 0.474 Chirality : 0.048 0.135 540 Planarity : 0.008 0.071 660 Dihedral : 7.791 28.867 510 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.64 % Allowed : 30.77 % Favored : 68.59 % Rotamer: Outliers : 4.80 % Allowed : 36.36 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.14 (0.24), residues: 468 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.68 (0.18), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.011 0.002 TYR F 88 PHE 0.023 0.004 PHE B 37 TRP 0.015 0.003 TRP D 92 HIS 0.003 0.001 HIS E 86 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3672) covalent geometry : angle 0.87983 ( 4998) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.73683 ( 12) hydrogen bonds : bond 0.02395 ( 18) hydrogen bonds : angle 6.02367 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.05 seconds wall clock time: 24 minutes 39.27 seconds (1479.27 seconds total)