Starting phenix.real_space_refine on Wed Sep 17 04:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3q_63824/09_2025/9u3q_63824.map" } resolution = 3.37 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= 0.004 sd= 0.042 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 27 5.16 5 C 2548 2.51 5 N 621 2.21 5 O 657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3853 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3853 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 3 Time building chain proxies: 1.24, per 1000 atoms: 0.32 Number of scatterers: 3853 At special positions: 0 Unit cell: (56.88, 77.42, 102.7, 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 27 16.00 O 657 8.00 N 621 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 268 " 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: 0.30 Conformation dependent library (CDL) restraints added in 141.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.565A pdb=" N LEU A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.878A pdb=" N ALA A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.084A pdb=" N ALA A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 removed outlier: 4.654A pdb=" N PHE A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.694A pdb=" N CYS A 217 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 removed outlier: 3.720A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 273 through 333 removed outlier: 3.670A pdb=" N HIS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 756 through 774 removed outlier: 4.360A pdb=" N TYR A 767 " --> pdb=" O TYR A 763 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 812 removed outlier: 3.571A pdb=" N LYS A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 809 " --> pdb=" O CYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 Processing helix chain 'A' and resid 849 through 860 Processing helix chain 'A' and resid 861 through 874 removed outlier: 3.502A pdb=" N ILE A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 882 removed outlier: 3.594A pdb=" N TYR A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.536A pdb=" N GLU A 889 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 908 removed outlier: 3.848A pdb=" N VAL A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 916 through 939 removed outlier: 3.506A pdb=" N SER A 922 " --> pdb=" O TRP A 918 " (cutoff:3.500A) Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 975 through 1032 312 hydrogen bonds defined for protein. 927 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: 0.59 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1165 1.34 - 1.46: 992 1.46 - 1.58: 1762 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 3958 Sorted by residual: bond pdb=" C ALA A 147 " pdb=" N PRO A 148 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.92e+00 bond pdb=" CA ASN A 911 " pdb=" CB ASN A 911 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.61e-02 3.86e+03 7.84e-01 bond pdb=" N THR A 813 " pdb=" CA THR A 813 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.44e-01 bond pdb=" CG1 ILE A 904 " pdb=" CD1 ILE A 904 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.32e-01 bond pdb=" CA PHE A 844 " pdb=" C PHE A 844 " ideal model delta sigma weight residual 1.532 1.525 0.008 9.60e-03 1.09e+04 6.68e-01 ... (remaining 3953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 5233 1.58 - 3.17: 118 3.17 - 4.75: 20 4.75 - 6.34: 6 6.34 - 7.92: 5 Bond angle restraints: 5382 Sorted by residual: angle pdb=" CB MET A 145 " pdb=" CG MET A 145 " pdb=" SD MET A 145 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" C ALA A 812 " pdb=" N THR A 813 " pdb=" CA THR A 813 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.44e+00 angle pdb=" N ILE A 228 " pdb=" CA ILE A 228 " pdb=" C ILE A 228 " ideal model delta sigma weight residual 111.45 109.14 2.31 9.30e-01 1.16e+00 6.16e+00 angle pdb=" CA ASN A 911 " pdb=" CB ASN A 911 " pdb=" CG ASN A 911 " ideal model delta sigma weight residual 112.60 114.98 -2.38 1.00e+00 1.00e+00 5.68e+00 angle pdb=" CB MET A 238 " pdb=" CG MET A 238 " pdb=" SD MET A 238 " ideal model delta sigma weight residual 112.70 119.58 -6.88 3.00e+00 1.11e-01 5.26e+00 ... (remaining 5377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1981 17.60 - 35.20: 244 35.20 - 52.80: 68 52.80 - 70.40: 11 70.40 - 88.00: 4 Dihedral angle restraints: 2308 sinusoidal: 885 harmonic: 1423 Sorted by residual: dihedral pdb=" CG ARG A 141 " pdb=" CD ARG A 141 " pdb=" NE ARG A 141 " pdb=" CZ ARG A 141 " ideal model delta sinusoidal sigma weight residual 90.00 134.94 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 770 " pdb=" CG GLU A 770 " pdb=" CD GLU A 770 " pdb=" OE1 GLU A 770 " ideal model delta sinusoidal sigma weight residual 0.00 -88.00 88.00 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB MET A 301 " pdb=" CG MET A 301 " pdb=" SD MET A 301 " pdb=" CE MET A 301 " ideal model delta sinusoidal sigma weight residual 60.00 117.04 -57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 2305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 413 0.030 - 0.060: 160 0.060 - 0.091: 38 0.091 - 0.121: 13 0.121 - 0.151: 5 Chirality restraints: 629 Sorted by residual: chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CG LEU A 179 " pdb=" CB LEU A 179 " pdb=" CD1 LEU A 179 " pdb=" CD2 LEU A 179 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA THR A 813 " pdb=" N THR A 813 " pdb=" C THR A 813 " pdb=" CB THR A 813 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 626 not shown) Planarity restraints: 655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 930 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO A 931 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 931 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 931 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 994 " -0.011 2.00e-02 2.50e+03 1.10e-02 3.04e+00 pdb=" CG TRP A 994 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 994 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 994 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 994 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 994 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 994 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 994 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 994 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 994 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 241 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.017 5.00e-02 4.00e+02 ... (remaining 652 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 35 2.67 - 3.23: 3911 3.23 - 3.78: 6152 3.78 - 4.34: 8286 4.34 - 4.90: 13248 Nonbonded interactions: 31632 Sorted by model distance: nonbonded pdb=" OD1 ASN A 911 " pdb=" N PHE A 912 " model vdw 2.109 3.120 nonbonded pdb=" NH2 ARG A 920 " pdb=" OD1 ASN A 997 " model vdw 2.172 3.120 nonbonded pdb=" NH1 ARG A 141 " pdb=" O GLN A 193 " model vdw 2.279 3.120 nonbonded pdb=" O PHE A 232 " pdb=" OG1 THR A 236 " model vdw 2.283 3.040 nonbonded pdb=" NH2 ARG A 141 " pdb=" O VAL A 194 " model vdw 2.309 3.120 ... (remaining 31627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.410 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.620 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 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 0.033 3959 Z= 0.123 Angle : 0.621 7.922 5384 Z= 0.325 Chirality : 0.036 0.151 629 Planarity : 0.004 0.059 655 Dihedral : 16.933 88.001 1379 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.69 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 22.70 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.39), residues: 474 helix: 1.55 (0.26), residues: 387 sheet: None (None), residues: 0 loop : 1.34 (0.76), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.017 0.002 TYR A 763 PHE 0.011 0.001 PHE A 798 TRP 0.030 0.002 TRP A 994 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3958) covalent geometry : angle 0.62102 ( 5382) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.49175 ( 2) hydrogen bonds : bond 0.24998 ( 312) hydrogen bonds : angle 7.62312 ( 927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.6022 (mmm) cc_final: 0.5742 (mmm) REVERT: A 223 SER cc_start: 0.8313 (p) cc_final: 0.8085 (t) REVERT: A 765 THR cc_start: 0.5901 (p) cc_final: 0.5623 (p) REVERT: A 849 MET cc_start: 0.1856 (ptp) cc_final: -0.1450 (mtt) REVERT: A 983 VAL cc_start: 0.8177 (t) cc_final: 0.7738 (m) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0500 time to fit residues: 5.1851 Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.214802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.191326 restraints weight = 5788.142| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 2.23 r_work: 0.4315 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3959 Z= 0.162 Angle : 0.585 6.767 5384 Z= 0.305 Chirality : 0.040 0.173 629 Planarity : 0.005 0.058 655 Dihedral : 3.895 17.302 519 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.48 % Favored : 98.31 % Rotamer: Outliers : 3.31 % Allowed : 18.68 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.37), residues: 474 helix: 2.03 (0.24), residues: 389 sheet: None (None), residues: 0 loop : 1.71 (0.76), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.014 0.002 TYR A 767 PHE 0.014 0.002 PHE A 792 TRP 0.019 0.001 TRP A 994 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3958) covalent geometry : angle 0.58471 ( 5382) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.62436 ( 2) hydrogen bonds : bond 0.04916 ( 312) hydrogen bonds : angle 4.54986 ( 927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.121 Fit side-chains REVERT: A 145 MET cc_start: 0.6342 (mmm) cc_final: 0.6132 (mmm) REVERT: A 258 THR cc_start: 0.4631 (OUTLIER) cc_final: 0.3654 (p) REVERT: A 849 MET cc_start: 0.3548 (ptp) cc_final: -0.1126 (mtt) REVERT: A 1022 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6036 (mp10) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.0466 time to fit residues: 5.6646 Evaluate side-chains 84 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1022 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 0.0370 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.215729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.191958 restraints weight = 5713.728| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 2.23 r_work: 0.4327 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3959 Z= 0.131 Angle : 0.545 8.031 5384 Z= 0.281 Chirality : 0.038 0.133 629 Planarity : 0.004 0.054 655 Dihedral : 3.836 16.640 519 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.27 % Favored : 98.52 % Rotamer: Outliers : 3.55 % Allowed : 19.86 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.27 (0.37), residues: 474 helix: 2.30 (0.25), residues: 386 sheet: None (None), residues: 0 loop : 1.76 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.015 0.002 TYR A 252 PHE 0.017 0.001 PHE A 792 TRP 0.015 0.001 TRP A 994 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3958) covalent geometry : angle 0.54527 ( 5382) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.52864 ( 2) hydrogen bonds : bond 0.03904 ( 312) hydrogen bonds : angle 4.15618 ( 927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.148 Fit side-chains REVERT: A 145 MET cc_start: 0.6478 (mmm) cc_final: 0.6257 (mmm) REVERT: A 280 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4673 (tp30) REVERT: A 1008 TYR cc_start: 0.7249 (t80) cc_final: 0.6909 (t80) REVERT: A 1022 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5861 (mp10) outliers start: 15 outliers final: 4 residues processed: 88 average time/residue: 0.0502 time to fit residues: 5.8987 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 1022 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 768 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 = 0.4703 r_free = 0.4703 target = 0.214505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.190534 restraints weight = 5684.687| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.23 r_work: 0.4313 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3959 Z= 0.130 Angle : 0.521 7.922 5384 Z= 0.266 Chirality : 0.038 0.132 629 Planarity : 0.004 0.052 655 Dihedral : 3.787 14.540 519 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.05 % Favored : 98.73 % Rotamer: Outliers : 3.55 % Allowed : 21.28 % Favored : 75.18 % 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 aren not related in a simple way. whole: 3.34 (0.37), residues: 474 helix: 2.40 (0.25), residues: 387 sheet: None (None), residues: 0 loop : 1.52 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.012 0.002 TYR A 172 PHE 0.013 0.001 PHE A 792 TRP 0.012 0.001 TRP A 994 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3958) covalent geometry : angle 0.52106 ( 5382) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.39056 ( 2) hydrogen bonds : bond 0.03628 ( 312) hydrogen bonds : angle 3.96164 ( 927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.144 Fit side-chains REVERT: A 1022 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5838 (mp10) outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 0.0491 time to fit residues: 5.4530 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 1022 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 768 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 = 0.4700 r_free = 0.4700 target = 0.214082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.190154 restraints weight = 5717.408| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 2.23 r_work: 0.4318 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3959 Z= 0.124 Angle : 0.516 7.171 5384 Z= 0.260 Chirality : 0.037 0.132 629 Planarity : 0.004 0.049 655 Dihedral : 3.730 14.104 519 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.27 % Favored : 98.52 % Rotamer: Outliers : 3.31 % Allowed : 21.75 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.37), residues: 474 helix: 2.51 (0.25), residues: 388 sheet: None (None), residues: 0 loop : 1.48 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.008 0.001 TYR A 261 PHE 0.018 0.001 PHE A 792 TRP 0.012 0.001 TRP A 994 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3958) covalent geometry : angle 0.51641 ( 5382) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.37114 ( 2) hydrogen bonds : bond 0.03475 ( 312) hydrogen bonds : angle 3.86244 ( 927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.4662 (OUTLIER) cc_final: 0.4402 (tp30) REVERT: A 1022 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.5840 (mp10) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.0456 time to fit residues: 5.1153 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 768 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 = 0.4694 r_free = 0.4694 target = 0.213196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.189112 restraints weight = 5771.534| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.23 r_work: 0.4303 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3959 Z= 0.142 Angle : 0.559 7.091 5384 Z= 0.287 Chirality : 0.038 0.133 629 Planarity : 0.004 0.049 655 Dihedral : 3.804 17.286 519 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.69 % Favored : 98.10 % Rotamer: Outliers : 3.78 % Allowed : 20.57 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.37), residues: 474 helix: 2.48 (0.24), residues: 392 sheet: None (None), residues: 0 loop : 1.49 (0.81), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 107 TYR 0.021 0.002 TYR A 168 PHE 0.017 0.001 PHE A 792 TRP 0.011 0.001 TRP A 994 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3958) covalent geometry : angle 0.55924 ( 5382) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.37411 ( 2) hydrogen bonds : bond 0.03562 ( 312) hydrogen bonds : angle 3.92271 ( 927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.4394 (tp30) REVERT: A 849 MET cc_start: 0.3043 (ptp) cc_final: -0.1606 (mtt) REVERT: A 1019 THR cc_start: 0.7697 (m) cc_final: 0.6711 (m) REVERT: A 1022 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5849 (mp10) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.0507 time to fit residues: 5.5020 Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 768 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 = 0.4705 r_free = 0.4705 target = 0.214180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.189897 restraints weight = 5833.996| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.24 r_work: 0.4308 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3959 Z= 0.129 Angle : 0.539 6.222 5384 Z= 0.277 Chirality : 0.038 0.131 629 Planarity : 0.004 0.047 655 Dihedral : 3.764 16.375 519 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.69 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 21.04 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.37), residues: 474 helix: 2.58 (0.24), residues: 392 sheet: None (None), residues: 0 loop : 1.40 (0.78), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 107 TYR 0.026 0.002 TYR A 909 PHE 0.019 0.001 PHE A 792 TRP 0.011 0.001 TRP A 994 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3958) covalent geometry : angle 0.53886 ( 5382) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.34651 ( 2) hydrogen bonds : bond 0.03403 ( 312) hydrogen bonds : angle 3.87847 ( 927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.4358 (tp30) REVERT: A 912 PHE cc_start: 0.7265 (m-10) cc_final: 0.6955 (m-10) REVERT: A 1019 THR cc_start: 0.7640 (m) cc_final: 0.7130 (m) REVERT: A 1022 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6089 (mp10) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.0488 time to fit residues: 5.4598 Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS ** A 768 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 = 0.4712 r_free = 0.4712 target = 0.214811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.190427 restraints weight = 5777.922| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 2.24 r_work: 0.4313 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3959 Z= 0.121 Angle : 0.529 6.469 5384 Z= 0.273 Chirality : 0.037 0.132 629 Planarity : 0.004 0.046 655 Dihedral : 3.733 16.603 519 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.90 % Favored : 97.89 % Rotamer: Outliers : 4.26 % Allowed : 20.57 % Favored : 75.18 % 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 aren not related in a simple way. whole: 3.62 (0.37), residues: 474 helix: 2.61 (0.24), residues: 392 sheet: None (None), residues: 0 loop : 1.43 (0.77), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.040 0.002 TYR A 909 PHE 0.016 0.001 PHE A 792 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3958) covalent geometry : angle 0.52932 ( 5382) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.28439 ( 2) hydrogen bonds : bond 0.03319 ( 312) hydrogen bonds : angle 3.89239 ( 927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4058 (tp30) REVERT: A 927 VAL cc_start: 0.1623 (OUTLIER) cc_final: 0.1161 (m) REVERT: A 1019 THR cc_start: 0.7581 (m) cc_final: 0.7095 (m) REVERT: A 1022 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.6079 (mp10) outliers start: 18 outliers final: 11 residues processed: 83 average time/residue: 0.0454 time to fit residues: 5.3288 Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 HIS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1022 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS ** A 768 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 = 0.4696 r_free = 0.4696 target = 0.213248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.188592 restraints weight = 5828.881| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.25 r_work: 0.4292 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3959 Z= 0.157 Angle : 0.562 7.736 5384 Z= 0.289 Chirality : 0.039 0.165 629 Planarity : 0.004 0.048 655 Dihedral : 3.794 16.558 519 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.69 % Favored : 98.10 % Rotamer: Outliers : 4.73 % Allowed : 21.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.37 (0.37), residues: 474 helix: 2.44 (0.24), residues: 391 sheet: None (None), residues: 0 loop : 1.36 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.025 0.002 TYR A 909 PHE 0.022 0.001 PHE A 912 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3958) covalent geometry : angle 0.56227 ( 5382) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.35531 ( 2) hydrogen bonds : bond 0.03434 ( 312) hydrogen bonds : angle 3.99382 ( 927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.6671 (t80) cc_final: 0.6471 (t80) REVERT: A 280 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.4343 (tp30) REVERT: A 1019 THR cc_start: 0.7611 (m) cc_final: 0.6991 (m) REVERT: A 1022 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.6080 (mp10) outliers start: 20 outliers final: 13 residues processed: 87 average time/residue: 0.0477 time to fit residues: 5.6701 Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 HIS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS ** A 768 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 = 0.4699 r_free = 0.4699 target = 0.213625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189401 restraints weight = 5813.120| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.25 r_work: 0.4305 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3959 Z= 0.147 Angle : 0.567 7.321 5384 Z= 0.289 Chirality : 0.040 0.166 629 Planarity : 0.004 0.047 655 Dihedral : 3.850 16.348 519 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.55 % Allowed : 21.99 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.37), residues: 474 helix: 2.46 (0.24), residues: 391 sheet: None (None), residues: 0 loop : 1.31 (0.78), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.021 0.002 TYR A 909 PHE 0.041 0.002 PHE A 912 TRP 0.012 0.001 TRP A 994 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3958) covalent geometry : angle 0.56708 ( 5382) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.24943 ( 2) hydrogen bonds : bond 0.03366 ( 312) hydrogen bonds : angle 3.97507 ( 927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 121 PHE cc_start: 0.6647 (t80) cc_final: 0.6405 (t80) REVERT: A 280 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.4326 (tp30) REVERT: A 1019 THR cc_start: 0.7588 (m) cc_final: 0.6988 (m) REVERT: A 1022 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6058 (mp10) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.0512 time to fit residues: 5.5303 Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 262 HIS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1022 GLN Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 HIS ** A 768 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 = 0.4708 r_free = 0.4708 target = 0.214524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.190360 restraints weight = 5715.438| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 2.21 r_work: 0.4319 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3959 Z= 0.135 Angle : 0.551 7.040 5384 Z= 0.281 Chirality : 0.039 0.161 629 Planarity : 0.004 0.045 655 Dihedral : 3.812 16.245 519 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.07 % Allowed : 22.22 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.37), residues: 474 helix: 2.50 (0.24), residues: 392 sheet: None (None), residues: 0 loop : 1.26 (0.77), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.014 0.002 TYR A 168 PHE 0.040 0.001 PHE A 912 TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 3958) covalent geometry : angle 0.55076 ( 5382) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.22105 ( 2) hydrogen bonds : bond 0.03294 ( 312) hydrogen bonds : angle 3.92755 ( 927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 959.80 seconds wall clock time: 17 minutes 15.30 seconds (1035.30 seconds total)