Starting phenix.real_space_refine on Thu Sep 10 23:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.cif Found real_map, /net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.map" model { file = "/net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28ob_56665/09_2026/28ob_56665.cif" } resolution = 4.38 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= 0.002 sd= 0.041 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 25 5.16 5 C 3280 2.51 5 N 830 2.21 5 O 855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4990 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 998 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Restraints were copied for chains: C, D, E, B Time building chain proxies: 0.96, per 1000 atoms: 0.19 Number of scatterers: 4990 At special positions: 0 Unit cell: (74.74, 75.48, 119.88, 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 25 16.00 O 855 8.00 N 830 7.00 C 3280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 216.2 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.753A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 40 removed outlier: 4.096A pdb=" N VAL A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 74 through 106 removed outlier: 4.218A pdb=" N PHE A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 135 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 15 through 40 removed outlier: 4.096A pdb=" N VAL C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 74 through 106 removed outlier: 4.218A pdb=" N PHE C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 135 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 15 through 40 removed outlier: 4.096A pdb=" N VAL D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 74 through 106 removed outlier: 4.218A pdb=" N PHE D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 135 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 15 through 40 removed outlier: 4.096A pdb=" N VAL E 21 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 74 through 106 removed outlier: 4.218A pdb=" N PHE E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 135 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 15 through 40 removed outlier: 4.096A pdb=" N VAL B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 74 through 106 removed outlier: 4.218A pdb=" N PHE B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 135 395 hydrogen bonds defined for protein. 1185 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: 0.73 Time building geometry restraints manager: 0.58 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: 1585 1.34 - 1.46: 761 1.46 - 1.57: 2669 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 5065 Sorted by residual: bond pdb=" CB VAL B 88 " pdb=" CG1 VAL B 88 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.07e-01 bond pdb=" CB VAL D 88 " pdb=" CG1 VAL D 88 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.00e-01 bond pdb=" CB VAL C 88 " pdb=" CG1 VAL C 88 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.90e-01 bond pdb=" CB VAL A 88 " pdb=" CG1 VAL A 88 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.87e-01 bond pdb=" CB VAL E 88 " pdb=" CG1 VAL E 88 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.82e-01 ... (remaining 5060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 6478 1.26 - 2.52: 278 2.52 - 3.78: 44 3.78 - 5.04: 14 5.04 - 6.30: 6 Bond angle restraints: 6820 Sorted by residual: angle pdb=" N MET E 42 " pdb=" CA MET E 42 " pdb=" C MET E 42 " ideal model delta sigma weight residual 109.81 113.83 -4.02 2.21e+00 2.05e-01 3.31e+00 angle pdb=" N MET D 42 " pdb=" CA MET D 42 " pdb=" C MET D 42 " ideal model delta sigma weight residual 109.81 113.83 -4.02 2.21e+00 2.05e-01 3.30e+00 angle pdb=" N MET B 42 " pdb=" CA MET B 42 " pdb=" C MET B 42 " ideal model delta sigma weight residual 109.81 113.82 -4.01 2.21e+00 2.05e-01 3.29e+00 angle pdb=" N MET C 42 " pdb=" CA MET C 42 " pdb=" C MET C 42 " ideal model delta sigma weight residual 109.81 113.82 -4.01 2.21e+00 2.05e-01 3.29e+00 angle pdb=" N MET A 42 " pdb=" CA MET A 42 " pdb=" C MET A 42 " ideal model delta sigma weight residual 109.81 113.80 -3.99 2.21e+00 2.05e-01 3.27e+00 ... (remaining 6815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2750 17.88 - 35.77: 235 35.77 - 53.65: 90 53.65 - 71.53: 10 71.53 - 89.42: 5 Dihedral angle restraints: 3090 sinusoidal: 1255 harmonic: 1835 Sorted by residual: dihedral pdb=" CB GLU B 6 " pdb=" CG GLU B 6 " pdb=" CD GLU B 6 " pdb=" OE1 GLU B 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.42 -89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 6 " pdb=" CG GLU D 6 " pdb=" CD GLU D 6 " pdb=" OE1 GLU D 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.41 -89.41 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 6 " pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " pdb=" OE1 GLU C 6 " ideal model delta sinusoidal sigma weight residual 0.00 89.41 -89.41 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 444 0.023 - 0.047: 192 0.047 - 0.070: 113 0.070 - 0.093: 49 0.093 - 0.117: 22 Chirality restraints: 820 Sorted by residual: chirality pdb=" CA ILE B 3 " pdb=" N ILE B 3 " pdb=" C ILE B 3 " pdb=" CB ILE B 3 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA ILE D 3 " pdb=" N ILE D 3 " pdb=" C ILE D 3 " pdb=" CB ILE D 3 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 817 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 42 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 43 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 42 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO E 43 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 42 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 43 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 35 2.65 - 3.21: 5124 3.21 - 3.77: 7918 3.77 - 4.34: 9793 4.34 - 4.90: 15162 Nonbonded interactions: 38032 Sorted by model distance: nonbonded pdb=" OE1 GLU A 9 " pdb=" ND2 ASN C 100 " model vdw 2.088 3.120 nonbonded pdb=" OE1 GLU E 9 " pdb=" ND2 ASN B 100 " model vdw 2.271 3.120 nonbonded pdb=" O VAL C 77 " pdb=" ND2 ASN C 81 " model vdw 2.286 3.120 nonbonded pdb=" O VAL D 77 " pdb=" ND2 ASN D 81 " model vdw 2.286 3.120 nonbonded pdb=" O VAL E 77 " pdb=" ND2 ASN E 81 " model vdw 2.286 3.120 ... (remaining 38027 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.260 Find NCS groups from input model: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 0.026 5065 Z= 0.148 Angle : 0.621 6.304 6820 Z= 0.344 Chirality : 0.039 0.117 820 Planarity : 0.004 0.038 855 Dihedral : 15.894 89.418 1890 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.80 % Allowed : 9.35 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 620 helix: -0.49 (0.20), residues: 470 sheet: None (None), residues: 0 loop : -1.11 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 8 TYR 0.002 0.001 TYR A 75 PHE 0.006 0.001 PHE D 93 HIS 0.003 0.002 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 5065) covalent geometry : angle 0.62111 / 0.34 ( 6820) hydrogen bonds : bond 0.10641 / 7.52 ( 395) hydrogen bonds : angle 4.59987 / 3.38 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 289 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.8595 (t80) cc_final: 0.8125 (t80) REVERT: A 41 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (tp) REVERT: A 100 ASN cc_start: 0.8898 (t0) cc_final: 0.8336 (t0) REVERT: A 119 GLU cc_start: 0.9273 (tt0) cc_final: 0.8849 (tt0) REVERT: A 124 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8209 (mt-10) REVERT: C 119 GLU cc_start: 0.9171 (tt0) cc_final: 0.8770 (tt0) REVERT: C 124 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 8 ARG cc_start: 0.9199 (ttp80) cc_final: 0.8975 (ptm160) REVERT: D 41 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8491 (tp) REVERT: D 100 ASN cc_start: 0.8922 (t0) cc_final: 0.8363 (t0) REVERT: D 119 GLU cc_start: 0.9239 (tt0) cc_final: 0.8951 (tt0) REVERT: D 124 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8217 (mt-10) REVERT: E 7 PHE cc_start: 0.8486 (t80) cc_final: 0.8043 (t80) REVERT: E 41 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8475 (tp) REVERT: E 119 GLU cc_start: 0.9198 (tt0) cc_final: 0.8740 (tt0) REVERT: B 6 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8564 (tp30) outliers start: 15 outliers final: 9 residues processed: 292 average time/residue: 0.0884 time to fit residues: 31.6981 Evaluate side-chains 188 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN D 74 HIS D 103 ASN E 74 HIS ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN B 80 GLN B 103 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098511 restraints weight = 12750.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101556 restraints weight = 8519.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103644 restraints weight = 6373.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105204 restraints weight = 5187.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106299 restraints weight = 4452.590| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5065 Z= 0.135 Angle : 0.600 6.352 6820 Z= 0.322 Chirality : 0.039 0.148 820 Planarity : 0.004 0.039 855 Dihedral : 4.435 14.463 665 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.75 % Allowed : 4.11 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.32), residues: 620 helix: 0.67 (0.22), residues: 475 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 104 TYR 0.009 0.002 TYR D 75 PHE 0.019 0.001 PHE D 83 HIS 0.003 0.002 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 5065) covalent geometry : angle 0.59971 / 0.32 ( 6820) hydrogen bonds : bond 0.03989 / 2.72 ( 395) hydrogen bonds : angle 3.78405 / 2.80 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.8712 (t80) cc_final: 0.8262 (t80) REVERT: A 42 MET cc_start: 0.8645 (tmm) cc_final: 0.8233 (tmm) REVERT: A 57 PHE cc_start: 0.7084 (t80) cc_final: 0.6753 (t80) REVERT: A 119 GLU cc_start: 0.9224 (tt0) cc_final: 0.8852 (tt0) REVERT: A 124 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8162 (mt-10) REVERT: C 42 MET cc_start: 0.8522 (tmm) cc_final: 0.8267 (tmm) REVERT: C 57 PHE cc_start: 0.7126 (t80) cc_final: 0.6772 (t80) REVERT: C 74 HIS cc_start: 0.8619 (m-70) cc_final: 0.7823 (m90) REVERT: C 124 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8221 (mt-10) REVERT: D 1 MET cc_start: 0.4569 (pmm) cc_final: 0.2888 (mpp) REVERT: D 19 LEU cc_start: 0.9533 (tt) cc_final: 0.9267 (tt) REVERT: D 42 MET cc_start: 0.8626 (tmm) cc_final: 0.8354 (tmm) REVERT: D 74 HIS cc_start: 0.8533 (m-70) cc_final: 0.8236 (m90) REVERT: D 119 GLU cc_start: 0.9174 (tt0) cc_final: 0.8936 (tt0) REVERT: D 124 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8195 (mt-10) REVERT: E 7 PHE cc_start: 0.8679 (t80) cc_final: 0.8218 (t80) REVERT: E 41 ILE cc_start: 0.8631 (pt) cc_final: 0.8166 (tp) REVERT: E 78 PHE cc_start: 0.9219 (t80) cc_final: 0.9011 (t80) REVERT: E 80 GLN cc_start: 0.8589 (tp40) cc_final: 0.8382 (tp-100) REVERT: E 100 ASN cc_start: 0.8838 (t0) cc_final: 0.8623 (t0) REVERT: E 119 GLU cc_start: 0.9167 (tt0) cc_final: 0.8811 (tt0) REVERT: E 124 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8153 (mt-10) REVERT: E 127 ASP cc_start: 0.8552 (m-30) cc_final: 0.8314 (m-30) REVERT: E 134 ASN cc_start: 0.8472 (t0) cc_final: 0.8176 (t0) REVERT: B 8 ARG cc_start: 0.8875 (ptm160) cc_final: 0.8584 (ptt180) REVERT: B 12 MET cc_start: 0.8454 (mtt) cc_final: 0.8144 (mmm) outliers start: 4 outliers final: 4 residues processed: 252 average time/residue: 0.0673 time to fit residues: 21.9926 Evaluate side-chains 177 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 5 optimal weight: 0.0470 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 133 ASN C 103 ASN D 103 ASN B 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101243 restraints weight = 12460.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104373 restraints weight = 8163.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106531 restraints weight = 6016.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108205 restraints weight = 4853.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109396 restraints weight = 4135.259| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5065 Z= 0.136 Angle : 0.626 6.484 6820 Z= 0.333 Chirality : 0.041 0.158 820 Planarity : 0.004 0.040 855 Dihedral : 4.447 14.447 665 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.32), residues: 620 helix: 1.19 (0.22), residues: 475 sheet: None (None), residues: 0 loop : -0.29 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.015 0.002 TYR B 75 PHE 0.021 0.001 PHE E 83 HIS 0.006 0.003 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 5065) covalent geometry : angle 0.62613 / 0.33 ( 6820) hydrogen bonds : bond 0.03868 / 2.67 ( 395) hydrogen bonds : angle 3.65569 / 2.72 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.8702 (t80) cc_final: 0.8352 (t80) REVERT: A 42 MET cc_start: 0.8595 (tmm) cc_final: 0.8241 (tmm) REVERT: A 57 PHE cc_start: 0.7189 (t80) cc_final: 0.6868 (t80) REVERT: A 119 GLU cc_start: 0.9217 (tt0) cc_final: 0.8884 (tt0) REVERT: A 124 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8226 (mt-10) REVERT: C 1 MET cc_start: 0.4970 (pmm) cc_final: 0.3301 (mpp) REVERT: C 12 MET cc_start: 0.8739 (mtt) cc_final: 0.8523 (ttm) REVERT: C 57 PHE cc_start: 0.7154 (t80) cc_final: 0.6883 (t80) REVERT: C 74 HIS cc_start: 0.8505 (m-70) cc_final: 0.7930 (m-70) REVERT: C 119 GLU cc_start: 0.9120 (tt0) cc_final: 0.8755 (tt0) REVERT: C 124 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8255 (mt-10) REVERT: D 1 MET cc_start: 0.4727 (pmm) cc_final: 0.3469 (mpp) REVERT: D 42 MET cc_start: 0.8669 (tmm) cc_final: 0.8372 (tmm) REVERT: D 57 PHE cc_start: 0.7227 (t80) cc_final: 0.6868 (t80) REVERT: D 74 HIS cc_start: 0.8568 (m-70) cc_final: 0.8214 (m-70) REVERT: D 119 GLU cc_start: 0.9185 (tt0) cc_final: 0.8923 (tt0) REVERT: D 124 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8251 (mt-10) REVERT: E 7 PHE cc_start: 0.8694 (t80) cc_final: 0.8387 (t80) REVERT: E 57 PHE cc_start: 0.7191 (t80) cc_final: 0.6838 (t80) REVERT: E 119 GLU cc_start: 0.9166 (tt0) cc_final: 0.8813 (tt0) REVERT: E 123 THR cc_start: 0.9092 (p) cc_final: 0.8772 (p) REVERT: E 124 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8216 (mt-10) REVERT: E 134 ASN cc_start: 0.8501 (t0) cc_final: 0.8234 (t0) REVERT: B 8 ARG cc_start: 0.8838 (ptm160) cc_final: 0.8566 (ptt180) REVERT: B 12 MET cc_start: 0.8389 (mtt) cc_final: 0.8143 (mmm) REVERT: B 57 PHE cc_start: 0.6924 (t80) cc_final: 0.6637 (t80) REVERT: B 119 GLU cc_start: 0.9075 (tt0) cc_final: 0.8779 (pt0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.0683 time to fit residues: 20.1455 Evaluate side-chains 173 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN B 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097074 restraints weight = 12695.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100100 restraints weight = 8513.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102320 restraints weight = 6371.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103888 restraints weight = 5163.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104544 restraints weight = 4441.020| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5065 Z= 0.144 Angle : 0.664 8.943 6820 Z= 0.348 Chirality : 0.041 0.143 820 Planarity : 0.004 0.040 855 Dihedral : 4.503 15.643 665 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.32), residues: 620 helix: 1.22 (0.22), residues: 475 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.009 0.002 TYR D 75 PHE 0.012 0.002 PHE A 83 HIS 0.006 0.003 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5065) covalent geometry : angle 0.66359 / 0.35 ( 6820) hydrogen bonds : bond 0.03944 / 2.75 ( 395) hydrogen bonds : angle 3.76718 / 2.80 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.8588 (tmm) cc_final: 0.8315 (tmm) REVERT: A 57 PHE cc_start: 0.7316 (t80) cc_final: 0.6978 (t80) REVERT: A 119 GLU cc_start: 0.9204 (tt0) cc_final: 0.8894 (tt0) REVERT: A 124 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8248 (mt-10) REVERT: C 1 MET cc_start: 0.5138 (pmm) cc_final: 0.2959 (mtt) REVERT: C 8 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8351 (ptt180) REVERT: C 12 MET cc_start: 0.8675 (mtt) cc_final: 0.8292 (ttm) REVERT: C 57 PHE cc_start: 0.7312 (t80) cc_final: 0.7003 (t80) REVERT: C 74 HIS cc_start: 0.8601 (m-70) cc_final: 0.7935 (m-70) REVERT: C 119 GLU cc_start: 0.9170 (tt0) cc_final: 0.8871 (tt0) REVERT: C 123 THR cc_start: 0.9142 (p) cc_final: 0.8842 (t) REVERT: C 124 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 6 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8250 (mm-30) REVERT: D 12 MET cc_start: 0.8573 (mmt) cc_final: 0.8361 (mmm) REVERT: D 57 PHE cc_start: 0.7403 (t80) cc_final: 0.7011 (t80) REVERT: D 74 HIS cc_start: 0.8617 (m-70) cc_final: 0.8386 (m-70) REVERT: D 81 ASN cc_start: 0.8725 (m-40) cc_final: 0.8504 (m110) REVERT: D 119 GLU cc_start: 0.9177 (tt0) cc_final: 0.8922 (tt0) REVERT: D 124 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8264 (mt-10) REVERT: E 57 PHE cc_start: 0.7304 (t80) cc_final: 0.6928 (t80) REVERT: E 119 GLU cc_start: 0.9193 (tt0) cc_final: 0.8950 (tt0) REVERT: E 124 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8290 (mt-10) REVERT: E 134 ASN cc_start: 0.8375 (t0) cc_final: 0.8100 (t0) REVERT: B 12 MET cc_start: 0.8338 (mtt) cc_final: 0.7875 (tpt) REVERT: B 119 GLU cc_start: 0.9075 (tt0) cc_final: 0.8791 (pt0) REVERT: B 124 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 126 ARG cc_start: 0.8917 (tmm160) cc_final: 0.8662 (ptm-80) REVERT: B 127 ASP cc_start: 0.8610 (m-30) cc_final: 0.8280 (m-30) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0626 time to fit residues: 18.7169 Evaluate side-chains 172 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.3980 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 132 GLN A 134 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN B 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097390 restraints weight = 13139.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100336 restraints weight = 9132.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102403 restraints weight = 7004.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103946 restraints weight = 5788.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104921 restraints weight = 5029.707| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5065 Z= 0.134 Angle : 0.634 9.762 6820 Z= 0.336 Chirality : 0.040 0.154 820 Planarity : 0.004 0.041 855 Dihedral : 4.498 15.762 665 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.33), residues: 620 helix: 1.37 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -0.17 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.012 0.002 TYR A 75 PHE 0.018 0.001 PHE B 83 HIS 0.005 0.003 HIS E 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5065) covalent geometry : angle 0.63419 / 0.34 ( 6820) hydrogen bonds : bond 0.03827 / 2.67 ( 395) hydrogen bonds : angle 3.76467 / 2.79 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.8639 (m-70) cc_final: 0.8085 (m-70) REVERT: A 119 GLU cc_start: 0.9193 (tt0) cc_final: 0.8892 (tt0) REVERT: A 124 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8335 (mt-10) REVERT: C 1 MET cc_start: 0.4973 (pmm) cc_final: 0.2830 (mtt) REVERT: C 8 ARG cc_start: 0.8577 (ptm160) cc_final: 0.8258 (ptt180) REVERT: C 12 MET cc_start: 0.8607 (mtt) cc_final: 0.8217 (ttm) REVERT: C 57 PHE cc_start: 0.7349 (t80) cc_final: 0.7011 (t80) REVERT: C 74 HIS cc_start: 0.8492 (m-70) cc_final: 0.8118 (m-70) REVERT: C 123 THR cc_start: 0.9135 (p) cc_final: 0.8835 (t) REVERT: C 124 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8291 (mt-10) REVERT: D 1 MET cc_start: 0.5241 (pmm) cc_final: 0.3027 (mtt) REVERT: D 74 HIS cc_start: 0.8486 (m-70) cc_final: 0.8221 (m-70) REVERT: D 81 ASN cc_start: 0.8689 (m-40) cc_final: 0.8425 (m110) REVERT: D 104 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.8016 (ptm-80) REVERT: D 119 GLU cc_start: 0.9206 (tt0) cc_final: 0.8956 (tt0) REVERT: D 124 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8246 (mt-10) REVERT: E 42 MET cc_start: 0.8590 (tmm) cc_final: 0.8275 (tmm) REVERT: E 57 PHE cc_start: 0.7291 (t80) cc_final: 0.6938 (t80) REVERT: E 119 GLU cc_start: 0.9217 (tt0) cc_final: 0.8960 (tt0) REVERT: E 123 THR cc_start: 0.9048 (p) cc_final: 0.8730 (p) REVERT: E 134 ASN cc_start: 0.8342 (t0) cc_final: 0.8087 (t0) REVERT: B 57 PHE cc_start: 0.7162 (t80) cc_final: 0.6758 (t80) REVERT: B 119 GLU cc_start: 0.9036 (tt0) cc_final: 0.8801 (pt0) REVERT: B 126 ARG cc_start: 0.8957 (tmm160) cc_final: 0.8679 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0622 time to fit residues: 19.1514 Evaluate side-chains 186 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN E 103 ASN B 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.128868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097283 restraints weight = 12861.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100333 restraints weight = 8560.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102456 restraints weight = 6372.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104114 restraints weight = 5160.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105080 restraints weight = 4389.838| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5065 Z= 0.145 Angle : 0.677 9.549 6820 Z= 0.361 Chirality : 0.042 0.159 820 Planarity : 0.004 0.041 855 Dihedral : 4.547 16.058 665 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.33), residues: 620 helix: 1.25 (0.23), residues: 475 sheet: None (None), residues: 0 loop : -0.16 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 104 TYR 0.015 0.002 TYR A 75 PHE 0.018 0.002 PHE C 83 HIS 0.006 0.003 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 5065) covalent geometry : angle 0.67716 / 0.36 ( 6820) hydrogen bonds : bond 0.03864 / 2.73 ( 395) hydrogen bonds : angle 3.89087 / 2.91 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8826 (pt) cc_final: 0.8612 (pt) REVERT: A 45 LEU cc_start: 0.8772 (tp) cc_final: 0.8539 (pp) REVERT: A 57 PHE cc_start: 0.7216 (t80) cc_final: 0.6725 (t80) REVERT: A 74 HIS cc_start: 0.8650 (m-70) cc_final: 0.8306 (m-70) REVERT: A 119 GLU cc_start: 0.9235 (tt0) cc_final: 0.8907 (tt0) REVERT: C 1 MET cc_start: 0.5115 (pmm) cc_final: 0.2724 (mtt) REVERT: C 8 ARG cc_start: 0.8576 (ptm160) cc_final: 0.8221 (ptt180) REVERT: C 12 MET cc_start: 0.8530 (mtt) cc_final: 0.8132 (ttm) REVERT: C 54 PHE cc_start: 0.8550 (m-80) cc_final: 0.8145 (m-10) REVERT: C 57 PHE cc_start: 0.7241 (t80) cc_final: 0.6928 (t80) REVERT: C 74 HIS cc_start: 0.8475 (m-70) cc_final: 0.8220 (m-70) REVERT: C 81 ASN cc_start: 0.8866 (m-40) cc_final: 0.8561 (m-40) REVERT: C 119 GLU cc_start: 0.9187 (tt0) cc_final: 0.8824 (tt0) REVERT: C 124 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8331 (mt-10) REVERT: D 8 ARG cc_start: 0.8691 (ptm160) cc_final: 0.8365 (ptt180) REVERT: D 57 PHE cc_start: 0.7417 (t80) cc_final: 0.6968 (t80) REVERT: D 74 HIS cc_start: 0.8567 (m-70) cc_final: 0.8284 (m-70) REVERT: D 81 ASN cc_start: 0.8801 (m-40) cc_final: 0.8493 (m110) REVERT: D 123 THR cc_start: 0.9108 (p) cc_final: 0.8673 (t) REVERT: D 124 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8199 (mt-10) REVERT: D 126 ARG cc_start: 0.8854 (tmm160) cc_final: 0.8631 (ptm-80) REVERT: D 127 ASP cc_start: 0.8713 (m-30) cc_final: 0.8306 (m-30) REVERT: E 57 PHE cc_start: 0.7276 (t80) cc_final: 0.6978 (t80) REVERT: E 74 HIS cc_start: 0.8610 (m-70) cc_final: 0.8147 (m-70) REVERT: E 80 GLN cc_start: 0.9120 (tt0) cc_final: 0.8343 (tp40) REVERT: E 119 GLU cc_start: 0.9200 (tt0) cc_final: 0.8816 (tt0) REVERT: E 126 ARG cc_start: 0.9135 (tmt170) cc_final: 0.8778 (ptm-80) REVERT: E 134 ASN cc_start: 0.8327 (t0) cc_final: 0.8094 (t0) REVERT: B 57 PHE cc_start: 0.7053 (t80) cc_final: 0.6815 (t80) REVERT: B 119 GLU cc_start: 0.9132 (tt0) cc_final: 0.8818 (pt0) REVERT: B 126 ARG cc_start: 0.8986 (tmm160) cc_final: 0.8700 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0620 time to fit residues: 19.7317 Evaluate side-chains 188 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 0.0060 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.0060 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 0.4612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097723 restraints weight = 12727.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100669 restraints weight = 8718.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102824 restraints weight = 6629.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104386 restraints weight = 5421.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105126 restraints weight = 4692.909| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5065 Z= 0.135 Angle : 0.670 6.731 6820 Z= 0.359 Chirality : 0.042 0.176 820 Planarity : 0.004 0.041 855 Dihedral : 4.576 14.850 665 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.33), residues: 620 helix: 1.19 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -0.48 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.013 0.002 TYR B 75 PHE 0.020 0.002 PHE E 83 HIS 0.006 0.003 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5065) covalent geometry : angle 0.67043 / 0.36 ( 6820) hydrogen bonds : bond 0.03858 / 2.68 ( 395) hydrogen bonds : angle 3.88293 / 2.88 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 PHE cc_start: 0.8413 (m-10) cc_final: 0.8098 (m-10) REVERT: A 57 PHE cc_start: 0.7114 (t80) cc_final: 0.6865 (t80) REVERT: A 74 HIS cc_start: 0.8478 (m-70) cc_final: 0.8233 (m-70) REVERT: A 81 ASN cc_start: 0.8874 (m-40) cc_final: 0.8661 (m110) REVERT: A 119 GLU cc_start: 0.9209 (tt0) cc_final: 0.8897 (tt0) REVERT: C 1 MET cc_start: 0.4985 (pmm) cc_final: 0.2671 (mtt) REVERT: C 8 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8182 (ptt180) REVERT: C 12 MET cc_start: 0.8517 (mtt) cc_final: 0.8148 (ttm) REVERT: C 57 PHE cc_start: 0.7348 (t80) cc_final: 0.6946 (t80) REVERT: C 74 HIS cc_start: 0.8389 (m-70) cc_final: 0.7973 (m-70) REVERT: C 78 PHE cc_start: 0.9191 (t80) cc_final: 0.8910 (t80) REVERT: C 81 ASN cc_start: 0.8765 (m-40) cc_final: 0.8518 (m110) REVERT: C 119 GLU cc_start: 0.9196 (tt0) cc_final: 0.8882 (tt0) REVERT: C 123 THR cc_start: 0.9111 (p) cc_final: 0.8778 (t) REVERT: C 124 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 1 MET cc_start: 0.5670 (pmm) cc_final: 0.3167 (mtt) REVERT: D 8 ARG cc_start: 0.8782 (ptm160) cc_final: 0.8523 (ptt180) REVERT: D 36 LEU cc_start: 0.8832 (tt) cc_final: 0.8569 (tp) REVERT: D 57 PHE cc_start: 0.7164 (t80) cc_final: 0.6912 (t80) REVERT: D 80 GLN cc_start: 0.8891 (tt0) cc_final: 0.7909 (tp40) REVERT: D 81 ASN cc_start: 0.8678 (m-40) cc_final: 0.8413 (m110) REVERT: D 123 THR cc_start: 0.9077 (p) cc_final: 0.8714 (t) REVERT: D 124 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8224 (mt-10) REVERT: D 127 ASP cc_start: 0.8775 (m-30) cc_final: 0.8278 (m-30) REVERT: E 74 HIS cc_start: 0.8528 (m-70) cc_final: 0.8316 (m-70) REVERT: E 119 GLU cc_start: 0.9179 (tt0) cc_final: 0.8924 (tt0) REVERT: E 126 ARG cc_start: 0.9109 (tmt170) cc_final: 0.8894 (tmt-80) REVERT: E 134 ASN cc_start: 0.8342 (t0) cc_final: 0.8110 (t0) REVERT: B 12 MET cc_start: 0.8282 (mmt) cc_final: 0.8042 (mmp) REVERT: B 57 PHE cc_start: 0.7269 (t80) cc_final: 0.6881 (t80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.0643 time to fit residues: 21.0581 Evaluate side-chains 188 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 0.0050 chunk 46 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.099697 restraints weight = 12911.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102708 restraints weight = 8639.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104962 restraints weight = 6482.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106486 restraints weight = 5234.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107662 restraints weight = 4491.111| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5065 Z= 0.135 Angle : 0.676 8.231 6820 Z= 0.362 Chirality : 0.042 0.158 820 Planarity : 0.004 0.041 855 Dihedral : 4.562 17.887 665 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.33), residues: 620 helix: 1.20 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -0.57 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 104 TYR 0.013 0.002 TYR E 75 PHE 0.021 0.002 PHE B 7 HIS 0.005 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 5065) covalent geometry : angle 0.67562 / 0.36 ( 6820) hydrogen bonds : bond 0.03796 / 2.65 ( 395) hydrogen bonds : angle 3.88587 / 2.87 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8884 (pt) cc_final: 0.8649 (pt) REVERT: A 42 MET cc_start: 0.8619 (tmm) cc_final: 0.8291 (tmm) REVERT: A 45 LEU cc_start: 0.8740 (tp) cc_final: 0.8526 (pp) REVERT: A 54 PHE cc_start: 0.8381 (m-10) cc_final: 0.7241 (m-10) REVERT: A 57 PHE cc_start: 0.7267 (t80) cc_final: 0.6819 (t80) REVERT: A 74 HIS cc_start: 0.8445 (m-70) cc_final: 0.8127 (m-70) REVERT: A 119 GLU cc_start: 0.9185 (tt0) cc_final: 0.8853 (tt0) REVERT: A 126 ARG cc_start: 0.9113 (tmt170) cc_final: 0.8801 (tmt-80) REVERT: C 1 MET cc_start: 0.4984 (pmm) cc_final: 0.2411 (mtt) REVERT: C 8 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8136 (ptt180) REVERT: C 12 MET cc_start: 0.8341 (mtt) cc_final: 0.7944 (ttm) REVERT: C 57 PHE cc_start: 0.7161 (t80) cc_final: 0.6857 (t80) REVERT: C 74 HIS cc_start: 0.8324 (m-70) cc_final: 0.8076 (m-70) REVERT: C 81 ASN cc_start: 0.8748 (m-40) cc_final: 0.8529 (m110) REVERT: C 119 GLU cc_start: 0.9248 (tt0) cc_final: 0.8865 (tt0) REVERT: C 124 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 36 LEU cc_start: 0.8852 (tt) cc_final: 0.8598 (tp) REVERT: D 57 PHE cc_start: 0.7327 (t80) cc_final: 0.6911 (t80) REVERT: D 81 ASN cc_start: 0.8782 (m-40) cc_final: 0.8484 (m110) REVERT: D 124 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8338 (mt-10) REVERT: E 119 GLU cc_start: 0.9171 (tt0) cc_final: 0.8806 (tt0) REVERT: E 126 ARG cc_start: 0.9139 (tmt170) cc_final: 0.8901 (tmt-80) REVERT: E 134 ASN cc_start: 0.8268 (t0) cc_final: 0.8022 (t0) REVERT: B 12 MET cc_start: 0.8244 (mmt) cc_final: 0.7969 (mmp) REVERT: B 57 PHE cc_start: 0.7135 (t80) cc_final: 0.6925 (t80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0609 time to fit residues: 19.5441 Evaluate side-chains 187 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN C 80 GLN C 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100023 restraints weight = 12698.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103000 restraints weight = 8657.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105102 restraints weight = 6543.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106675 restraints weight = 5338.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107770 restraints weight = 4577.645| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5065 Z= 0.135 Angle : 0.678 6.824 6820 Z= 0.373 Chirality : 0.042 0.173 820 Planarity : 0.004 0.039 855 Dihedral : 4.387 14.358 665 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.33), residues: 620 helix: 1.29 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -0.69 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 104 TYR 0.012 0.002 TYR D 75 PHE 0.025 0.001 PHE D 7 HIS 0.005 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5065) covalent geometry : angle 0.67781 / 0.37 ( 6820) hydrogen bonds : bond 0.03744 / 2.64 ( 395) hydrogen bonds : angle 3.95226 / 2.96 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8881 (pt) cc_final: 0.8649 (pt) REVERT: A 42 MET cc_start: 0.8647 (tmm) cc_final: 0.8358 (tmm) REVERT: A 45 LEU cc_start: 0.8717 (tp) cc_final: 0.8501 (pp) REVERT: A 54 PHE cc_start: 0.8395 (m-10) cc_final: 0.7275 (m-10) REVERT: A 74 HIS cc_start: 0.8400 (m-70) cc_final: 0.7924 (m-70) REVERT: A 119 GLU cc_start: 0.9167 (tt0) cc_final: 0.8841 (tt0) REVERT: A 124 GLU cc_start: 0.8363 (pt0) cc_final: 0.8072 (pt0) REVERT: C 8 ARG cc_start: 0.8496 (ptm160) cc_final: 0.8109 (ptt180) REVERT: C 12 MET cc_start: 0.8298 (mtt) cc_final: 0.7908 (ttm) REVERT: C 54 PHE cc_start: 0.8344 (m-80) cc_final: 0.8021 (m-10) REVERT: C 57 PHE cc_start: 0.7212 (t80) cc_final: 0.6807 (t80) REVERT: C 74 HIS cc_start: 0.8319 (m-70) cc_final: 0.8059 (m-70) REVERT: C 119 GLU cc_start: 0.9261 (tt0) cc_final: 0.8937 (tt0) REVERT: C 123 THR cc_start: 0.9108 (p) cc_final: 0.8639 (t) REVERT: C 124 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8049 (mt-10) REVERT: C 127 ASP cc_start: 0.8587 (m-30) cc_final: 0.8192 (m-30) REVERT: D 1 MET cc_start: 0.6012 (pmm) cc_final: 0.3181 (mtt) REVERT: D 36 LEU cc_start: 0.8852 (tt) cc_final: 0.8417 (tp) REVERT: D 81 ASN cc_start: 0.8737 (m-40) cc_final: 0.8429 (m110) REVERT: D 124 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8272 (mt-10) REVERT: E 54 PHE cc_start: 0.8436 (m-10) cc_final: 0.8232 (m-80) REVERT: E 119 GLU cc_start: 0.9126 (tt0) cc_final: 0.8769 (tt0) REVERT: E 126 ARG cc_start: 0.9122 (tmt170) cc_final: 0.8893 (tmt-80) REVERT: E 134 ASN cc_start: 0.8293 (t0) cc_final: 0.8070 (t0) REVERT: B 12 MET cc_start: 0.8219 (mmt) cc_final: 0.7947 (mmp) REVERT: B 57 PHE cc_start: 0.7279 (t80) cc_final: 0.7041 (t80) REVERT: B 119 GLU cc_start: 0.9069 (tt0) cc_final: 0.8787 (pt0) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0578 time to fit residues: 18.4737 Evaluate side-chains 191 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099696 restraints weight = 12707.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102652 restraints weight = 8498.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104849 restraints weight = 6362.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106399 restraints weight = 5128.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107362 restraints weight = 4390.465| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5065 Z= 0.135 Angle : 0.695 9.042 6820 Z= 0.381 Chirality : 0.042 0.174 820 Planarity : 0.004 0.040 855 Dihedral : 4.356 16.370 665 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.34), residues: 620 helix: 1.08 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.011 0.002 TYR D 75 PHE 0.028 0.002 PHE E 83 HIS 0.006 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 5065) covalent geometry : angle 0.69464 / 0.38 ( 6820) hydrogen bonds : bond 0.03846 / 2.71 ( 395) hydrogen bonds : angle 3.97969 / 3.01 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8905 (pt) cc_final: 0.8681 (pt) REVERT: A 45 LEU cc_start: 0.8711 (tp) cc_final: 0.8505 (pp) REVERT: A 73 MET cc_start: 0.7097 (mmm) cc_final: 0.6603 (mmt) REVERT: A 74 HIS cc_start: 0.8355 (m-70) cc_final: 0.8034 (m-70) REVERT: A 119 GLU cc_start: 0.9164 (tt0) cc_final: 0.8800 (tt0) REVERT: A 124 GLU cc_start: 0.8388 (pt0) cc_final: 0.8161 (pt0) REVERT: A 134 ASN cc_start: 0.8584 (t0) cc_final: 0.8381 (t0) REVERT: C 1 MET cc_start: 0.5069 (pmm) cc_final: 0.2249 (mtt) REVERT: C 8 ARG cc_start: 0.8536 (ptm160) cc_final: 0.8164 (ptt180) REVERT: C 12 MET cc_start: 0.8239 (mtt) cc_final: 0.7848 (ttm) REVERT: C 54 PHE cc_start: 0.8423 (m-80) cc_final: 0.8046 (m-10) REVERT: C 57 PHE cc_start: 0.7182 (t80) cc_final: 0.6806 (t80) REVERT: C 74 HIS cc_start: 0.8320 (m-70) cc_final: 0.7955 (m-70) REVERT: C 119 GLU cc_start: 0.9263 (tt0) cc_final: 0.8933 (tt0) REVERT: C 123 THR cc_start: 0.9100 (p) cc_final: 0.8607 (t) REVERT: C 124 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8036 (mt-10) REVERT: D 36 LEU cc_start: 0.8883 (tt) cc_final: 0.8519 (tp) REVERT: D 57 PHE cc_start: 0.6958 (t80) cc_final: 0.6734 (t80) REVERT: D 74 HIS cc_start: 0.8266 (m-70) cc_final: 0.8025 (m-70) REVERT: D 81 ASN cc_start: 0.8719 (m-40) cc_final: 0.8425 (m110) REVERT: D 124 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8252 (mt-10) REVERT: E 119 GLU cc_start: 0.9136 (tt0) cc_final: 0.8823 (tt0) REVERT: E 124 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8197 (pt0) REVERT: E 126 ARG cc_start: 0.9151 (tmt170) cc_final: 0.8879 (tmt-80) REVERT: B 12 MET cc_start: 0.8244 (mmt) cc_final: 0.7986 (mmp) REVERT: B 57 PHE cc_start: 0.7266 (t80) cc_final: 0.7004 (t80) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0621 time to fit residues: 19.8813 Evaluate side-chains 191 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099728 restraints weight = 12760.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102660 restraints weight = 8574.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104862 restraints weight = 6458.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106420 restraints weight = 5203.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107245 restraints weight = 4445.257| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5065 Z= 0.134 Angle : 0.688 7.249 6820 Z= 0.379 Chirality : 0.042 0.190 820 Planarity : 0.004 0.039 855 Dihedral : 4.210 15.533 665 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.34), residues: 620 helix: 1.13 (0.24), residues: 480 sheet: None (None), residues: 0 loop : -0.87 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 104 TYR 0.007 0.001 TYR B 75 PHE 0.020 0.001 PHE A 83 HIS 0.004 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 5065) covalent geometry : angle 0.68752 / 0.38 ( 6820) hydrogen bonds : bond 0.03781 / 2.68 ( 395) hydrogen bonds : angle 3.91446 / 2.96 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.25 seconds wall clock time: 19 minutes 18.05 seconds (1158.05 seconds total)