Starting phenix.real_space_refine on Tue Aug 4 16:29:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.cif Found real_map, /net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.map" model { file = "/net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26wc_80928/08_2026/26wc_80928.cif" } resolution = 3.63 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= 0.234 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 28 5.16 5 C 3002 2.51 5 N 774 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4768 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 656 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Restraints were copied for chains: a, h, l Time building chain proxies: 1.28, per 1000 atoms: 0.27 Number of scatterers: 4768 At special positions: 0 Unit cell: (128.4, 66, 62.4, 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 28 16.00 O 964 8.00 N 774 7.00 C 3002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 126 " - pdb=" SG CYS a 180 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " 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: 0.37 Conformation dependent library (CDL) restraints added in 180.3 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 8.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.589A pdb=" N GLU A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.900A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.527A pdb=" N MET L 83 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 118 through 129 removed outlier: 3.589A pdb=" N GLU a 129 " --> pdb=" O ASN a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 146 Processing helix chain 'h' and resid 62 through 65 removed outlier: 3.900A pdb=" N LYS h 65 " --> pdb=" O GLN h 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 62 through 65' Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.527A pdb=" N MET l 83 " --> pdb=" O TYR l 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 117 removed outlier: 7.057A pdb=" N ASP A 115 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR A 178 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.591A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR H 109 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR H 109 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR H 104 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.668A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.907A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.907A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'a' and resid 113 through 117 removed outlier: 7.057A pdb=" N ASP a 115 " --> pdb=" O TYR a 178 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR a 178 " --> pdb=" O ASP a 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.591A pdb=" N VAL h 18 " --> pdb=" O LEU h 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU h 83 " --> pdb=" O VAL h 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR h 71 " --> pdb=" O TYR h 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR h 112 " --> pdb=" O GLU h 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR h 109 " --> pdb=" O TYR h 94 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR h 112 " --> pdb=" O GLU h 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR h 109 " --> pdb=" O TYR h 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR h 104 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.668A pdb=" N SER l 7 " --> pdb=" O THR l 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.907A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.907A pdb=" N GLY l 84 " --> pdb=" O LEU l 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN l 90 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR l 97 " --> pdb=" O GLN l 90 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 372 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: 0.78 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1490 1.35 - 1.46: 1310 1.46 - 1.58: 2042 1.58 - 1.70: 0 1.70 - 1.81: 40 Bond restraints: 4882 Sorted by residual: bond pdb=" N HIS A 182 " pdb=" CA HIS A 182 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.17e-02 7.31e+03 4.21e+00 bond pdb=" N HIS a 182 " pdb=" CA HIS a 182 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.17e-02 7.31e+03 4.21e+00 bond pdb=" C THR A 181 " pdb=" N HIS A 182 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.60e-02 3.91e+03 4.04e+00 bond pdb=" C THR a 181 " pdb=" N HIS a 182 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.60e-02 3.91e+03 4.04e+00 bond pdb=" CA HIS A 182 " pdb=" CB HIS A 182 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.49e-02 4.50e+03 8.28e-01 ... (remaining 4877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 6382 1.10 - 2.21: 180 2.21 - 3.31: 34 3.31 - 4.41: 6 4.41 - 5.52: 8 Bond angle restraints: 6610 Sorted by residual: angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" C ALA L 51 " ideal model delta sigma weight residual 110.80 116.12 -5.32 2.13e+00 2.20e-01 6.24e+00 angle pdb=" N ALA l 51 " pdb=" CA ALA l 51 " pdb=" C ALA l 51 " ideal model delta sigma weight residual 110.80 116.12 -5.32 2.13e+00 2.20e-01 6.24e+00 angle pdb=" C THR A 160 " pdb=" N LYS A 161 " pdb=" CA LYS A 161 " ideal model delta sigma weight residual 121.54 126.04 -4.50 1.91e+00 2.74e-01 5.56e+00 angle pdb=" C THR a 160 " pdb=" N LYS a 161 " pdb=" CA LYS a 161 " ideal model delta sigma weight residual 121.54 126.04 -4.50 1.91e+00 2.74e-01 5.56e+00 angle pdb=" N VAL a 139 " pdb=" CA VAL a 139 " pdb=" C VAL a 139 " ideal model delta sigma weight residual 112.29 110.07 2.22 9.40e-01 1.13e+00 5.56e+00 ... (remaining 6605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 2558 15.16 - 30.33: 244 30.33 - 45.49: 54 45.49 - 60.65: 12 60.65 - 75.82: 12 Dihedral angle restraints: 2880 sinusoidal: 1104 harmonic: 1776 Sorted by residual: dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 88 " pdb=" CB CYS l 88 " ideal model delta sinusoidal sigma weight residual 93.00 153.17 -60.17 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 153.17 -60.17 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ARG l 50 " pdb=" C ARG l 50 " pdb=" N ALA l 51 " pdb=" CA ALA l 51 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 2877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 380 0.025 - 0.050: 236 0.050 - 0.074: 36 0.074 - 0.099: 28 0.099 - 0.123: 26 Chirality restraints: 706 Sorted by residual: chirality pdb=" CA ILE l 75 " pdb=" N ILE l 75 " pdb=" C ILE l 75 " pdb=" CB ILE l 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL H 20 " pdb=" N VAL H 20 " pdb=" C VAL H 20 " pdb=" CB VAL H 20 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 703 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR a 181 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR a 181 " 0.057 2.00e-02 2.50e+03 pdb=" O THR a 181 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS a 182 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 181 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR A 181 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 181 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS A 182 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO L 59 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.016 5.00e-02 4.00e+02 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 3204 3.09 - 3.54: 4458 3.54 - 3.99: 6900 3.99 - 4.45: 8032 4.45 - 4.90: 13517 Nonbonded interactions: 36111 Sorted by model distance: nonbonded pdb=" N VAL A 148 " pdb=" N GLU A 149 " model vdw 2.636 2.560 nonbonded pdb=" N VAL a 148 " pdb=" N GLU a 149 " model vdw 2.636 2.560 nonbonded pdb=" N VAL a 139 " pdb=" N LEU a 140 " model vdw 2.645 2.560 nonbonded pdb=" N VAL A 139 " pdb=" N LEU A 140 " model vdw 2.645 2.560 nonbonded pdb=" N SER l 65 " pdb=" O SER l 65 " model vdw 2.649 2.496 ... (remaining 36106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.630 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.002 0.032 4888 Z= 0.116 Angle : 0.503 5.519 6622 Z= 0.280 Chirality : 0.038 0.123 706 Planarity : 0.003 0.033 834 Dihedral : 13.363 75.816 1738 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.59 (0.36), residues: 594 helix: -0.73 (0.95), residues: 38 sheet: -0.24 (0.36), residues: 236 loop : -0.35 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.001 TYR a 178 PHE 0.018 0.001 PHE A 179 TRP 0.005 0.001 TRP a 143 HIS 0.001 0.000 HIS H 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.12 ( 4882) covalent geometry : angle 0.50206 / 0.28 ( 6610) SS BOND : bond 0.00186 / 0.11 ( 6) SS BOND : angle 0.76962 / 0.42 ( 12) hydrogen bonds : bond 0.27439 / 18.17 ( 138) hydrogen bonds : angle 11.03492 / 7.85 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8964 (tp) cc_final: 0.8682 (tp) REVERT: H 35 TYR cc_start: 0.8550 (m-80) cc_final: 0.7687 (m-80) REVERT: H 36 TRP cc_start: 0.7604 (m100) cc_final: 0.7216 (m100) REVERT: H 46 GLU cc_start: 0.7924 (mp0) cc_final: 0.7626 (mp0) REVERT: H 55 ASN cc_start: 0.9238 (t0) cc_final: 0.8985 (t0) REVERT: H 80 TYR cc_start: 0.8516 (m-80) cc_final: 0.7977 (m-80) REVERT: H 111 LEU cc_start: 0.9002 (tp) cc_final: 0.8754 (tp) REVERT: L 103 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8758 (ttmm) REVERT: L 104 LEU cc_start: 0.9054 (mp) cc_final: 0.8720 (mt) REVERT: a 145 ILE cc_start: 0.8995 (tp) cc_final: 0.8710 (tp) REVERT: h 35 TYR cc_start: 0.8642 (m-80) cc_final: 0.8408 (m-80) REVERT: h 36 TRP cc_start: 0.7892 (m100) cc_final: 0.7579 (m100) REVERT: h 46 GLU cc_start: 0.7935 (mp0) cc_final: 0.7653 (mp0) REVERT: h 80 TYR cc_start: 0.8472 (m-80) cc_final: 0.7976 (m-80) REVERT: h 90 ASP cc_start: 0.8146 (m-30) cc_final: 0.7904 (m-30) REVERT: l 2 ILE cc_start: 0.9050 (mm) cc_final: 0.8814 (mm) REVERT: l 103 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8812 (ttmm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0703 time to fit residues: 18.9437 Evaluate side-chains 166 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN H 39 GLN H 61 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 173 GLN h 6 GLN h 39 GLN h 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059827 restraints weight = 15278.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061335 restraints weight = 6551.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062287 restraints weight = 3368.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062862 restraints weight = 1945.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063259 restraints weight = 1245.091| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4888 Z= 0.205 Angle : 0.640 5.561 6622 Z= 0.341 Chirality : 0.044 0.167 706 Planarity : 0.004 0.024 834 Dihedral : 5.070 27.052 664 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.26 % Allowed : 15.60 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.63 (0.36), residues: 594 helix: 0.22 (1.08), residues: 26 sheet: -0.34 (0.34), residues: 242 loop : -0.43 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.017 0.002 TYR l 91 PHE 0.016 0.002 PHE a 179 TRP 0.011 0.001 TRP a 143 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 4882) covalent geometry : angle 0.63867 / 0.34 ( 6610) SS BOND : bond 0.00422 / 0.24 ( 6) SS BOND : angle 1.04263 / 0.60 ( 12) hydrogen bonds : bond 0.04415 / 2.85 ( 138) hydrogen bonds : angle 7.48844 / 5.26 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8770 (m-80) cc_final: 0.7837 (m-80) REVERT: H 36 TRP cc_start: 0.7925 (m100) cc_final: 0.7457 (m100) REVERT: H 46 GLU cc_start: 0.7670 (mp0) cc_final: 0.7331 (mp0) REVERT: H 55 ASN cc_start: 0.9329 (t0) cc_final: 0.9124 (t0) REVERT: H 111 LEU cc_start: 0.9016 (tp) cc_final: 0.8566 (tp) REVERT: L 2 ILE cc_start: 0.8784 (mm) cc_final: 0.8558 (mm) REVERT: L 83 MET cc_start: 0.7731 (mmp) cc_final: 0.7425 (mmp) REVERT: L 103 LYS cc_start: 0.9154 (ttmt) cc_final: 0.8892 (ttmm) REVERT: L 104 LEU cc_start: 0.9034 (mp) cc_final: 0.8593 (mt) REVERT: a 145 ILE cc_start: 0.9048 (tp) cc_final: 0.8687 (tp) REVERT: a 175 VAL cc_start: 0.9361 (t) cc_final: 0.9025 (p) REVERT: h 36 TRP cc_start: 0.8231 (m100) cc_final: 0.7656 (m100) REVERT: h 46 GLU cc_start: 0.7683 (mp0) cc_final: 0.7350 (mp0) REVERT: h 51 ILE cc_start: 0.9209 (tt) cc_final: 0.8976 (pt) REVERT: h 94 TYR cc_start: 0.8034 (m-80) cc_final: 0.7659 (m-10) REVERT: l 2 ILE cc_start: 0.9023 (mm) cc_final: 0.8794 (mm) REVERT: l 83 MET cc_start: 0.7685 (mmp) cc_final: 0.7308 (mmp) REVERT: l 104 LEU cc_start: 0.8913 (mp) cc_final: 0.8425 (mt) outliers start: 12 outliers final: 5 residues processed: 173 average time/residue: 0.0664 time to fit residues: 15.0326 Evaluate side-chains 159 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 181 THR Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain l residue 11 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS H 61 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059330 restraints weight = 15417.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060821 restraints weight = 6459.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061734 restraints weight = 3234.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062289 restraints weight = 1816.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062623 restraints weight = 1120.613| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4888 Z= 0.203 Angle : 0.657 7.231 6622 Z= 0.347 Chirality : 0.044 0.163 706 Planarity : 0.003 0.025 834 Dihedral : 5.361 28.415 664 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.88 % Allowed : 18.23 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.70 (0.36), residues: 594 helix: -0.10 (1.06), residues: 26 sheet: -0.47 (0.34), residues: 242 loop : -0.38 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 50 TYR 0.018 0.002 TYR l 91 PHE 0.014 0.002 PHE H 29 TRP 0.014 0.001 TRP a 143 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 4882) covalent geometry : angle 0.64599 / 0.34 ( 6610) SS BOND : bond 0.00524 / 0.27 ( 6) SS BOND : angle 2.88255 / 1.72 ( 12) hydrogen bonds : bond 0.04040 / 2.56 ( 138) hydrogen bonds : angle 6.85300 / 4.78 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8847 (m-80) cc_final: 0.7777 (m-80) REVERT: H 36 TRP cc_start: 0.7957 (m100) cc_final: 0.7448 (m100) REVERT: H 46 GLU cc_start: 0.7639 (mp0) cc_final: 0.7263 (mp0) REVERT: L 2 ILE cc_start: 0.8690 (mm) cc_final: 0.8410 (mm) REVERT: L 83 MET cc_start: 0.7711 (mmp) cc_final: 0.7485 (mmp) REVERT: L 103 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8943 (ttmm) REVERT: L 104 LEU cc_start: 0.9011 (mp) cc_final: 0.8487 (mt) REVERT: a 145 ILE cc_start: 0.9039 (tp) cc_final: 0.8781 (tp) REVERT: a 175 VAL cc_start: 0.9328 (t) cc_final: 0.9046 (p) REVERT: h 36 TRP cc_start: 0.8307 (m100) cc_final: 0.7632 (m100) REVERT: h 46 GLU cc_start: 0.7572 (mp0) cc_final: 0.7208 (mp0) REVERT: l 1 ASP cc_start: 0.7206 (p0) cc_final: 0.6601 (p0) REVERT: l 2 ILE cc_start: 0.8958 (mm) cc_final: 0.8692 (mm) REVERT: l 3 GLN cc_start: 0.8378 (mm110) cc_final: 0.8029 (mm-40) REVERT: l 83 MET cc_start: 0.7645 (mmp) cc_final: 0.7418 (mmp) REVERT: l 104 LEU cc_start: 0.8918 (mp) cc_final: 0.8353 (mt) outliers start: 10 outliers final: 7 residues processed: 163 average time/residue: 0.0691 time to fit residues: 14.6526 Evaluate side-chains 157 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 11 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.065113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.060318 restraints weight = 15792.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061999 restraints weight = 6508.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063030 restraints weight = 3253.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063692 restraints weight = 1852.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064113 restraints weight = 1138.251| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4888 Z= 0.125 Angle : 0.590 7.068 6622 Z= 0.307 Chirality : 0.041 0.150 706 Planarity : 0.003 0.024 834 Dihedral : 4.962 29.888 664 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.76 % Allowed : 19.36 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.60 (0.36), residues: 594 helix: -0.13 (1.10), residues: 26 sheet: -0.24 (0.35), residues: 238 loop : -0.45 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 176 TYR 0.016 0.001 TYR h 35 PHE 0.008 0.001 PHE a 179 TRP 0.009 0.001 TRP h 47 HIS 0.001 0.000 HIS h 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 4882) covalent geometry : angle 0.58583 / 0.30 ( 6610) SS BOND : bond 0.00405 / 0.21 ( 6) SS BOND : angle 1.83253 / 1.09 ( 12) hydrogen bonds : bond 0.03180 / 2.04 ( 138) hydrogen bonds : angle 6.07974 / 4.25 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 VAL cc_start: 0.9352 (t) cc_final: 0.9130 (p) REVERT: H 35 TYR cc_start: 0.8834 (m-80) cc_final: 0.7697 (m-80) REVERT: H 46 GLU cc_start: 0.7575 (mp0) cc_final: 0.7061 (mp0) REVERT: H 81 MET cc_start: 0.8493 (tpt) cc_final: 0.7895 (tpt) REVERT: L 1 ASP cc_start: 0.7444 (p0) cc_final: 0.7231 (p0) REVERT: L 2 ILE cc_start: 0.8589 (mm) cc_final: 0.8280 (mm) REVERT: L 3 GLN cc_start: 0.8289 (mm110) cc_final: 0.8015 (mm110) REVERT: L 4 MET cc_start: 0.8212 (ttm) cc_final: 0.7914 (ttm) REVERT: L 83 MET cc_start: 0.7692 (mmp) cc_final: 0.7445 (mmp) REVERT: L 103 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8892 (ttmm) REVERT: a 175 VAL cc_start: 0.9393 (t) cc_final: 0.9091 (p) REVERT: h 36 TRP cc_start: 0.8361 (m100) cc_final: 0.7656 (m100) REVERT: h 46 GLU cc_start: 0.7572 (mp0) cc_final: 0.7024 (mp0) REVERT: h 55 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.9102 (t0) REVERT: l 1 ASP cc_start: 0.7167 (p0) cc_final: 0.6595 (p0) REVERT: l 2 ILE cc_start: 0.8944 (mm) cc_final: 0.8554 (mm) REVERT: l 3 GLN cc_start: 0.8488 (mm110) cc_final: 0.7981 (mm-40) REVERT: l 104 LEU cc_start: 0.8774 (mp) cc_final: 0.8228 (mt) outliers start: 20 outliers final: 8 residues processed: 174 average time/residue: 0.0726 time to fit residues: 16.3078 Evaluate side-chains 161 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 55 ASN Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057343 restraints weight = 15755.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058963 restraints weight = 6412.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059997 restraints weight = 3206.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.060680 restraints weight = 1824.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.061060 restraints weight = 1120.721| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 4888 Z= 0.263 Angle : 0.733 7.956 6622 Z= 0.382 Chirality : 0.046 0.176 706 Planarity : 0.003 0.026 834 Dihedral : 5.749 28.633 664 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.57 % Allowed : 23.87 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.94 (0.36), residues: 594 helix: 0.02 (1.15), residues: 24 sheet: -0.47 (0.35), residues: 238 loop : -0.72 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG l 53 TYR 0.019 0.002 TYR L 91 PHE 0.020 0.003 PHE h 29 TRP 0.017 0.002 TRP a 143 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 ( 4882) covalent geometry : angle 0.72544 / 0.38 ( 6610) SS BOND : bond 0.00460 / 0.25 ( 6) SS BOND : angle 2.58337 / 1.54 ( 12) hydrogen bonds : bond 0.04436 / 2.81 ( 138) hydrogen bonds : angle 6.57635 / 4.61 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8900 (tp) cc_final: 0.8568 (tp) REVERT: A 174 GLU cc_start: 0.7894 (tt0) cc_final: 0.7504 (tt0) REVERT: H 35 TYR cc_start: 0.8890 (m-80) cc_final: 0.7588 (m-80) REVERT: H 46 GLU cc_start: 0.7668 (mp0) cc_final: 0.7126 (mp0) REVERT: H 94 TYR cc_start: 0.7945 (m-80) cc_final: 0.7713 (m-10) REVERT: L 1 ASP cc_start: 0.7463 (p0) cc_final: 0.7257 (p0) REVERT: L 2 ILE cc_start: 0.8765 (mm) cc_final: 0.8258 (mm) REVERT: L 3 GLN cc_start: 0.8399 (mm110) cc_final: 0.8051 (mm110) REVERT: L 83 MET cc_start: 0.7754 (mmp) cc_final: 0.7367 (mmp) REVERT: a 145 ILE cc_start: 0.8930 (tp) cc_final: 0.8572 (tp) REVERT: h 36 TRP cc_start: 0.8369 (m100) cc_final: 0.7658 (m100) REVERT: h 46 GLU cc_start: 0.7618 (mp0) cc_final: 0.7063 (mp0) REVERT: h 55 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9136 (t0) REVERT: l 1 ASP cc_start: 0.7287 (p0) cc_final: 0.6707 (p0) REVERT: l 2 ILE cc_start: 0.8975 (mm) cc_final: 0.8540 (mm) REVERT: l 3 GLN cc_start: 0.8658 (mm110) cc_final: 0.8177 (mm-40) outliers start: 19 outliers final: 16 residues processed: 164 average time/residue: 0.0704 time to fit residues: 14.8150 Evaluate side-chains 163 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 159 ILE Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 55 ASN Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 11 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.065438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060542 restraints weight = 15979.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062241 restraints weight = 6522.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063297 restraints weight = 3258.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063857 restraints weight = 1832.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064304 restraints weight = 1189.385| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4888 Z= 0.125 Angle : 0.620 7.819 6622 Z= 0.319 Chirality : 0.041 0.155 706 Planarity : 0.003 0.023 834 Dihedral : 5.104 31.186 664 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.76 % Allowed : 23.68 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.84 (0.35), residues: 594 helix: 0.15 (1.18), residues: 24 sheet: -0.41 (0.35), residues: 238 loop : -0.65 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 50 TYR 0.016 0.002 TYR h 35 PHE 0.007 0.001 PHE a 179 TRP 0.009 0.001 TRP h 47 HIS 0.002 0.000 HIS h 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 4882) covalent geometry : angle 0.61656 / 0.32 ( 6610) SS BOND : bond 0.00523 / 0.26 ( 6) SS BOND : angle 1.60879 / 0.95 ( 12) hydrogen bonds : bond 0.03120 / 2.00 ( 138) hydrogen bonds : angle 5.64769 / 3.98 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8837 (m-80) cc_final: 0.7598 (m-80) REVERT: H 46 GLU cc_start: 0.7603 (mp0) cc_final: 0.7086 (mp0) REVERT: H 81 MET cc_start: 0.8567 (tpt) cc_final: 0.7948 (tpt) REVERT: H 99 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7702 (ttp80) REVERT: L 2 ILE cc_start: 0.8625 (mm) cc_final: 0.8143 (mm) REVERT: L 76 SER cc_start: 0.8037 (t) cc_final: 0.7764 (t) REVERT: L 83 MET cc_start: 0.7724 (mmp) cc_final: 0.7514 (mmp) REVERT: L 103 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8945 (ttmm) REVERT: L 104 LEU cc_start: 0.8946 (mp) cc_final: 0.8455 (mt) REVERT: a 174 GLU cc_start: 0.7422 (tt0) cc_final: 0.7023 (tt0) REVERT: a 175 VAL cc_start: 0.9343 (t) cc_final: 0.9037 (p) REVERT: h 36 TRP cc_start: 0.8206 (m100) cc_final: 0.7709 (m100) REVERT: h 46 GLU cc_start: 0.7535 (mp0) cc_final: 0.6989 (mp0) REVERT: h 55 ASN cc_start: 0.9321 (OUTLIER) cc_final: 0.9091 (t0) REVERT: l 1 ASP cc_start: 0.7314 (p0) cc_final: 0.6756 (p0) REVERT: l 2 ILE cc_start: 0.8938 (mm) cc_final: 0.8622 (mm) REVERT: l 3 GLN cc_start: 0.8538 (mm110) cc_final: 0.8117 (mm-40) REVERT: l 105 GLU cc_start: 0.8466 (mp0) cc_final: 0.7860 (mp0) outliers start: 20 outliers final: 13 residues processed: 173 average time/residue: 0.0717 time to fit residues: 15.9478 Evaluate side-chains 168 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 55 ASN Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 11 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.063965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.059062 restraints weight = 15563.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060752 restraints weight = 6421.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061779 restraints weight = 3220.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062484 restraints weight = 1835.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.062878 restraints weight = 1119.856| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4888 Z= 0.180 Angle : 0.664 8.067 6622 Z= 0.343 Chirality : 0.043 0.164 706 Planarity : 0.003 0.024 834 Dihedral : 5.325 30.511 664 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.14 % Allowed : 24.25 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.93 (0.35), residues: 594 helix: 0.04 (1.17), residues: 24 sheet: -0.46 (0.34), residues: 238 loop : -0.71 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 176 TYR 0.021 0.002 TYR H 32 PHE 0.012 0.002 PHE h 29 TRP 0.013 0.001 TRP a 143 HIS 0.002 0.001 HIS H 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 4882) covalent geometry : angle 0.65999 / 0.34 ( 6610) SS BOND : bond 0.00519 / 0.26 ( 6) SS BOND : angle 1.86309 / 1.12 ( 12) hydrogen bonds : bond 0.03603 / 2.30 ( 138) hydrogen bonds : angle 5.82520 / 4.11 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.8873 (m-80) cc_final: 0.7579 (m-80) REVERT: H 46 GLU cc_start: 0.7641 (mp0) cc_final: 0.7085 (mp0) REVERT: L 76 SER cc_start: 0.8233 (t) cc_final: 0.7998 (t) REVERT: L 83 MET cc_start: 0.7713 (mmp) cc_final: 0.7483 (mmp) REVERT: L 103 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8965 (ttmm) REVERT: L 104 LEU cc_start: 0.8983 (mp) cc_final: 0.8596 (mt) REVERT: a 175 VAL cc_start: 0.9324 (t) cc_final: 0.8971 (p) REVERT: h 46 GLU cc_start: 0.7537 (mp0) cc_final: 0.6972 (mp0) REVERT: h 55 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.9123 (t0) REVERT: h 81 MET cc_start: 0.8721 (tpt) cc_final: 0.8222 (tpt) REVERT: l 1 ASP cc_start: 0.7345 (p0) cc_final: 0.6803 (p0) REVERT: l 2 ILE cc_start: 0.8970 (mm) cc_final: 0.8630 (mm) REVERT: l 3 GLN cc_start: 0.8570 (mm110) cc_final: 0.8125 (mm-40) outliers start: 22 outliers final: 19 residues processed: 173 average time/residue: 0.0729 time to fit residues: 16.1503 Evaluate side-chains 172 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 136 LYS Chi-restraints excluded: chain a residue 180 CYS Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 55 ASN Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 11 MET Chi-restraints excluded: chain l residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.065701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060762 restraints weight = 15700.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062486 restraints weight = 6480.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063539 restraints weight = 3225.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064206 restraints weight = 1820.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064643 restraints weight = 1119.636| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4888 Z= 0.130 Angle : 0.640 8.125 6622 Z= 0.325 Chirality : 0.042 0.156 706 Planarity : 0.003 0.023 834 Dihedral : 5.055 31.674 664 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.57 % Allowed : 24.62 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.89 (0.35), residues: 594 helix: 0.05 (1.18), residues: 24 sheet: -0.40 (0.34), residues: 238 loop : -0.72 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG l 53 TYR 0.023 0.002 TYR H 32 PHE 0.007 0.001 PHE H 29 TRP 0.009 0.001 TRP h 47 HIS 0.001 0.000 HIS H 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4882) covalent geometry : angle 0.63664 / 0.32 ( 6610) SS BOND : bond 0.00455 / 0.23 ( 6) SS BOND : angle 1.58234 / 0.94 ( 12) hydrogen bonds : bond 0.03142 / 2.01 ( 138) hydrogen bonds : angle 5.50568 / 3.90 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 VAL cc_start: 0.9304 (t) cc_final: 0.9064 (p) REVERT: H 35 TYR cc_start: 0.8831 (m-80) cc_final: 0.7610 (m-80) REVERT: H 46 GLU cc_start: 0.7587 (mp0) cc_final: 0.7074 (mp0) REVERT: H 81 MET cc_start: 0.8579 (tpt) cc_final: 0.8025 (tpt) REVERT: H 99 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7714 (ttp80) REVERT: L 42 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7931 (mmmm) REVERT: L 76 SER cc_start: 0.8095 (t) cc_final: 0.7894 (t) REVERT: L 103 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8952 (ttmm) REVERT: a 112 LEU cc_start: 0.9346 (tt) cc_final: 0.9055 (tp) REVERT: a 175 VAL cc_start: 0.9354 (t) cc_final: 0.9047 (p) REVERT: h 36 TRP cc_start: 0.8171 (m100) cc_final: 0.7599 (m100) REVERT: h 46 GLU cc_start: 0.7476 (mp0) cc_final: 0.6882 (mp0) REVERT: h 55 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9099 (t0) REVERT: h 94 TYR cc_start: 0.7828 (m-80) cc_final: 0.7528 (m-10) REVERT: l 1 ASP cc_start: 0.7349 (p0) cc_final: 0.6804 (p0) REVERT: l 2 ILE cc_start: 0.8950 (mm) cc_final: 0.8571 (mm) REVERT: l 3 GLN cc_start: 0.8549 (mm110) cc_final: 0.8090 (mm-40) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 0.0785 time to fit residues: 17.2291 Evaluate side-chains 170 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 180 CYS Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 55 ASN Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 11 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 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 = 0.3018 r_free = 0.3018 target = 0.063178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.058281 restraints weight = 15535.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059933 restraints weight = 6506.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060956 restraints weight = 3283.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061654 restraints weight = 1886.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062058 restraints weight = 1152.016| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4888 Z= 0.229 Angle : 0.746 8.345 6622 Z= 0.383 Chirality : 0.045 0.169 706 Planarity : 0.003 0.025 834 Dihedral : 5.565 31.091 664 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.95 % Allowed : 24.62 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.02 (0.35), residues: 594 helix: -0.07 (1.16), residues: 24 sheet: -0.59 (0.34), residues: 242 loop : -0.71 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 176 TYR 0.023 0.002 TYR H 32 PHE 0.017 0.002 PHE H 29 TRP 0.016 0.002 TRP a 143 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 4882) covalent geometry : angle 0.74180 / 0.38 ( 6610) SS BOND : bond 0.00592 / 0.30 ( 6) SS BOND : angle 2.05276 / 1.23 ( 12) hydrogen bonds : bond 0.04012 / 2.55 ( 138) hydrogen bonds : angle 6.04653 / 4.27 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 VAL cc_start: 0.9324 (t) cc_final: 0.9088 (p) REVERT: H 35 TYR cc_start: 0.8905 (m-80) cc_final: 0.7708 (m-80) REVERT: H 46 GLU cc_start: 0.7654 (mp0) cc_final: 0.7116 (mp0) REVERT: a 175 VAL cc_start: 0.9283 (t) cc_final: 0.8997 (p) REVERT: h 46 GLU cc_start: 0.7520 (mp0) cc_final: 0.6979 (mp0) REVERT: h 81 MET cc_start: 0.8797 (tpt) cc_final: 0.8267 (tpt) REVERT: l 1 ASP cc_start: 0.7321 (p0) cc_final: 0.6786 (p0) REVERT: l 2 ILE cc_start: 0.8980 (mm) cc_final: 0.8641 (mm) REVERT: l 3 GLN cc_start: 0.8568 (mm110) cc_final: 0.8147 (mm-40) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.0719 time to fit residues: 15.4333 Evaluate side-chains 163 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 180 CYS Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 52 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.0170 chunk 55 optimal weight: 0.3980 chunk 6 optimal weight: 0.0010 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... h 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061682 restraints weight = 15436.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.063416 restraints weight = 6416.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064500 restraints weight = 3202.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065163 restraints weight = 1794.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065615 restraints weight = 1108.716| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4888 Z= 0.125 Angle : 0.685 8.208 6622 Z= 0.345 Chirality : 0.041 0.151 706 Planarity : 0.003 0.022 834 Dihedral : 4.997 30.688 664 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.44 % Allowed : 26.13 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.75 (0.35), residues: 594 helix: 0.14 (1.21), residues: 24 sheet: -0.15 (0.35), residues: 228 loop : -0.75 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 50 TYR 0.026 0.002 TYR H 32 PHE 0.010 0.001 PHE A 179 TRP 0.009 0.001 TRP h 47 HIS 0.002 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 4882) covalent geometry : angle 0.68266 / 0.34 ( 6610) SS BOND : bond 0.00452 / 0.23 ( 6) SS BOND : angle 1.59864 / 0.94 ( 12) hydrogen bonds : bond 0.03051 / 1.94 ( 138) hydrogen bonds : angle 5.49520 / 3.88 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.8849 (t80) cc_final: 0.8583 (t80) REVERT: A 175 VAL cc_start: 0.9301 (t) cc_final: 0.9087 (p) REVERT: H 46 GLU cc_start: 0.7506 (mp0) cc_final: 0.6986 (mp0) REVERT: H 81 MET cc_start: 0.8484 (tpt) cc_final: 0.7974 (tpt) REVERT: L 103 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8695 (ttmm) REVERT: a 112 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9060 (tp) REVERT: a 176 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7197 (mtm-85) REVERT: h 36 TRP cc_start: 0.8156 (m100) cc_final: 0.7626 (m100) REVERT: h 45 LEU cc_start: 0.8868 (mp) cc_final: 0.8653 (mp) REVERT: h 46 GLU cc_start: 0.7420 (mp0) cc_final: 0.6540 (mp0) REVERT: h 94 TYR cc_start: 0.7822 (m-80) cc_final: 0.7607 (m-80) REVERT: l 1 ASP cc_start: 0.7337 (p0) cc_final: 0.6777 (p0) REVERT: l 2 ILE cc_start: 0.8937 (mm) cc_final: 0.8562 (mm) REVERT: l 3 GLN cc_start: 0.8548 (mm110) cc_final: 0.8075 (mm-40) REVERT: l 24 LYS cc_start: 0.8893 (mttp) cc_final: 0.8670 (mttm) outliers start: 13 outliers final: 11 residues processed: 175 average time/residue: 0.0824 time to fit residues: 18.3998 Evaluate side-chains 168 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 180 CYS Chi-restraints excluded: chain h residue 40 SER Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059466 restraints weight = 15652.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061152 restraints weight = 6478.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.062188 restraints weight = 3252.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062897 restraints weight = 1857.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063322 restraints weight = 1138.736| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4888 Z= 0.183 Angle : 0.743 8.221 6622 Z= 0.380 Chirality : 0.043 0.165 706 Planarity : 0.003 0.027 834 Dihedral : 5.388 31.893 664 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.20 % Allowed : 26.50 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.83 (0.35), residues: 594 helix: 0.07 (1.17), residues: 24 sheet: -0.25 (0.35), residues: 232 loop : -0.77 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG l 53 TYR 0.024 0.002 TYR H 32 PHE 0.012 0.002 PHE H 29 TRP 0.014 0.001 TRP a 143 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 4882) covalent geometry : angle 0.73822 / 0.38 ( 6610) SS BOND : bond 0.00589 / 0.31 ( 6) SS BOND : angle 2.11952 / 1.22 ( 12) hydrogen bonds : bond 0.03621 / 2.30 ( 138) hydrogen bonds : angle 5.80460 / 4.10 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.16 seconds wall clock time: 18 minutes 19.65 seconds (1099.65 seconds total)