Starting phenix.real_space_refine on Wed Aug 5 17:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.cif Found real_map, /net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.map" model { file = "/net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13hq_77071/08_2026/13hq_77071.cif" } resolution = 2.67 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= 0.009 sd= 0.059 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 8 5.16 5 C 6728 2.51 5 N 2040 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 10784 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1348 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 12, 'TRANS': 160} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.11, per 1000 atoms: 0.10 Number of scatterers: 10784 At special positions: 0 Unit cell: (112.145, 112.145, 65.8464, 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 8 16.00 O 2008 8.00 N 2040 7.00 C 6728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 269.5 milliseconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2608 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 33.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.540A pdb=" N GLU A 70 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 179 through 208 Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.540A pdb=" N GLU B 70 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 111 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 179 through 208 Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.539A pdb=" N GLU C 70 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 71 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 111 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 179 through 208 Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.539A pdb=" N GLU D 70 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 71 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 111 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 179 through 208 Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.540A pdb=" N GLU E 70 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER E 71 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 111 Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 179 through 208 Processing helix chain 'F' and resid 66 through 71 removed outlier: 3.540A pdb=" N GLU F 70 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER F 71 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 111 Processing helix chain 'F' and resid 141 through 144 Processing helix chain 'F' and resid 179 through 208 Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.540A pdb=" N GLU G 70 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER G 71 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 111 Processing helix chain 'G' and resid 141 through 144 Processing helix chain 'G' and resid 179 through 208 Processing helix chain 'H' and resid 66 through 71 removed outlier: 3.539A pdb=" N GLU H 70 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER H 71 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 111 Processing helix chain 'H' and resid 141 through 144 Processing helix chain 'H' and resid 179 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 38 current: chain 'A' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 91 current: chain 'A' and resid 146 through 157 removed outlier: 6.136A pdb=" N ARG A 157 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 163 " --> pdb=" O ARG A 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 174 current: chain 'B' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 91 current: chain 'B' and resid 146 through 157 removed outlier: 6.134A pdb=" N ARG B 157 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 163 " --> pdb=" O ARG B 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 174 current: chain 'C' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 91 current: chain 'C' and resid 146 through 157 removed outlier: 6.135A pdb=" N ARG C 157 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL C 163 " --> pdb=" O ARG C 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 174 current: chain 'D' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 82 through 91 current: chain 'D' and resid 146 through 157 removed outlier: 6.135A pdb=" N ARG D 157 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL D 163 " --> pdb=" O ARG D 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 174 current: chain 'E' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 82 through 91 current: chain 'E' and resid 146 through 157 removed outlier: 6.135A pdb=" N ARG E 157 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL E 163 " --> pdb=" O ARG E 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 174 current: chain 'F' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 82 through 91 current: chain 'F' and resid 146 through 157 removed outlier: 6.134A pdb=" N ARG F 157 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL F 163 " --> pdb=" O ARG F 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 174 current: chain 'G' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 82 through 91 current: chain 'G' and resid 146 through 157 removed outlier: 6.134A pdb=" N ARG G 157 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL G 163 " --> pdb=" O ARG G 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 162 through 174 current: chain 'H' and resid 82 through 91 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 82 through 91 current: chain 'H' and resid 146 through 157 removed outlier: 6.135A pdb=" N ARG H 157 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL H 163 " --> pdb=" O ARG H 157 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1200 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: 1.00 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3768 1.34 - 1.46: 1513 1.46 - 1.57: 5703 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 11000 Sorted by residual: bond pdb=" CG PRO C 96 " pdb=" CD PRO C 96 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.51e-01 bond pdb=" CG PRO D 96 " pdb=" CD PRO D 96 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.46e-01 bond pdb=" CG PRO H 96 " pdb=" CD PRO H 96 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.42e-01 bond pdb=" CG PRO B 96 " pdb=" CD PRO B 96 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.41e-01 bond pdb=" CG PRO A 96 " pdb=" CD PRO A 96 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.31e-01 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 14700 1.69 - 3.39: 170 3.39 - 5.08: 58 5.08 - 6.77: 8 6.77 - 8.47: 8 Bond angle restraints: 14944 Sorted by residual: angle pdb=" CB PRO H 174 " pdb=" CG PRO H 174 " pdb=" CD PRO H 174 " ideal model delta sigma weight residual 106.10 97.63 8.47 3.20e+00 9.77e-02 7.00e+00 angle pdb=" CB PRO D 174 " pdb=" CG PRO D 174 " pdb=" CD PRO D 174 " ideal model delta sigma weight residual 106.10 97.67 8.43 3.20e+00 9.77e-02 6.94e+00 angle pdb=" CB PRO G 174 " pdb=" CG PRO G 174 " pdb=" CD PRO G 174 " ideal model delta sigma weight residual 106.10 97.67 8.43 3.20e+00 9.77e-02 6.94e+00 angle pdb=" CB PRO A 174 " pdb=" CG PRO A 174 " pdb=" CD PRO A 174 " ideal model delta sigma weight residual 106.10 97.68 8.42 3.20e+00 9.77e-02 6.92e+00 angle pdb=" CB PRO C 174 " pdb=" CG PRO C 174 " pdb=" CD PRO C 174 " ideal model delta sigma weight residual 106.10 97.68 8.42 3.20e+00 9.77e-02 6.92e+00 ... (remaining 14939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 6212 14.91 - 29.82: 388 29.82 - 44.73: 88 44.73 - 59.64: 48 59.64 - 74.55: 8 Dihedral angle restraints: 6744 sinusoidal: 2736 harmonic: 4008 Sorted by residual: dihedral pdb=" CG ARG A 150 " pdb=" CD ARG A 150 " pdb=" NE ARG A 150 " pdb=" CZ ARG A 150 " ideal model delta sinusoidal sigma weight residual 180.00 136.41 43.59 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG G 150 " pdb=" CD ARG G 150 " pdb=" NE ARG G 150 " pdb=" CZ ARG G 150 " ideal model delta sinusoidal sigma weight residual 180.00 136.43 43.57 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual 180.00 136.46 43.54 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 6741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1025 0.030 - 0.060: 435 0.060 - 0.089: 83 0.089 - 0.119: 96 0.119 - 0.149: 9 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB THR F 138 " pdb=" CA THR F 138 " pdb=" OG1 THR F 138 " pdb=" CG2 THR F 138 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CB THR H 138 " pdb=" CA THR H 138 " pdb=" OG1 THR H 138 " pdb=" CG2 THR H 138 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CB THR A 138 " pdb=" CA THR A 138 " pdb=" OG1 THR A 138 " pdb=" CG2 THR A 138 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1645 not shown) Planarity restraints: 2000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 90 " 0.155 9.50e-02 1.11e+02 6.99e-02 3.59e+00 pdb=" NE ARG D 90 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 90 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 90 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 90 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 90 " 0.155 9.50e-02 1.11e+02 6.99e-02 3.58e+00 pdb=" NE ARG B 90 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 90 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 90 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 90 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 90 " -0.155 9.50e-02 1.11e+02 6.98e-02 3.57e+00 pdb=" NE ARG F 90 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG F 90 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 90 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 90 " -0.001 2.00e-02 2.50e+03 ... (remaining 1997 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 7245 3.08 - 3.54: 10290 3.54 - 3.99: 17773 3.99 - 4.45: 21761 4.45 - 4.90: 32421 Nonbonded interactions: 89490 Sorted by model distance: nonbonded pdb=" N ASP H 93 " pdb=" O ASP H 93 " model vdw 2.629 2.496 nonbonded pdb=" N ASP G 93 " pdb=" O ASP G 93 " model vdw 2.629 2.496 nonbonded pdb=" N ASP B 93 " pdb=" O ASP B 93 " model vdw 2.629 2.496 nonbonded pdb=" N ASP E 93 " pdb=" O ASP E 93 " model vdw 2.629 2.496 nonbonded pdb=" N ASP F 93 " pdb=" O ASP F 93 " model vdw 2.629 2.496 ... (remaining 89485 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.220 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.400 Find NCS groups from input model: 0.150 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:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 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 0.027 11000 Z= 0.098 Angle : 0.562 8.466 14944 Z= 0.276 Chirality : 0.040 0.149 1648 Planarity : 0.006 0.070 2000 Dihedral : 11.975 74.551 4136 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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 are not related in a simple way. whole: -0.78 (0.20), residues: 1352 helix: 0.52 (0.25), residues: 368 sheet: -1.29 (0.24), residues: 352 loop : -0.54 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 90 TYR 0.004 0.001 TYR B 151 PHE 0.007 0.001 PHE H 107 TRP 0.013 0.001 TRP B 91 HIS 0.001 0.000 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 (11000) covalent geometry : angle 0.56180 / 0.28 (14944) hydrogen bonds : bond 0.15793 / 10.31 ( 416) hydrogen bonds : angle 5.58598 / 3.86 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8357 (mm-30) REVERT: A 140 TYR cc_start: 0.9293 (m-80) cc_final: 0.9008 (m-80) REVERT: A 202 THR cc_start: 0.9614 (m) cc_final: 0.9341 (p) REVERT: B 70 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8366 (mm-30) REVERT: B 74 ILE cc_start: 0.9770 (mt) cc_final: 0.9538 (mp) REVERT: B 140 TYR cc_start: 0.9364 (m-80) cc_final: 0.9020 (m-80) REVERT: B 202 THR cc_start: 0.9586 (m) cc_final: 0.9298 (p) REVERT: C 70 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8465 (mm-30) REVERT: C 128 GLU cc_start: 0.9199 (tt0) cc_final: 0.8993 (tm-30) REVERT: C 140 TYR cc_start: 0.9365 (m-80) cc_final: 0.9068 (m-80) REVERT: C 202 THR cc_start: 0.9577 (m) cc_final: 0.9299 (p) REVERT: D 70 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8289 (mp0) REVERT: D 140 TYR cc_start: 0.9308 (m-80) cc_final: 0.9064 (m-80) REVERT: D 202 THR cc_start: 0.9574 (m) cc_final: 0.9257 (p) REVERT: E 70 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8400 (mm-30) REVERT: E 202 THR cc_start: 0.9608 (m) cc_final: 0.9332 (p) REVERT: F 70 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8529 (mm-30) REVERT: F 74 ILE cc_start: 0.9752 (mt) cc_final: 0.9504 (mp) REVERT: F 140 TYR cc_start: 0.9338 (m-80) cc_final: 0.9110 (m-80) REVERT: F 202 THR cc_start: 0.9580 (m) cc_final: 0.9292 (p) REVERT: G 70 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8407 (mm-30) REVERT: G 128 GLU cc_start: 0.9230 (tt0) cc_final: 0.9024 (tm-30) REVERT: G 194 LEU cc_start: 0.9843 (tt) cc_final: 0.9631 (tm) REVERT: G 202 THR cc_start: 0.9611 (m) cc_final: 0.9344 (p) REVERT: H 70 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8531 (mm-30) REVERT: H 74 ILE cc_start: 0.9743 (mt) cc_final: 0.9486 (mp) REVERT: H 99 LEU cc_start: 0.9631 (tp) cc_final: 0.9370 (tp) REVERT: H 140 TYR cc_start: 0.9350 (m-80) cc_final: 0.9030 (m-80) REVERT: H 202 THR cc_start: 0.9587 (m) cc_final: 0.9312 (p) REVERT: H 209 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8921 (mm-40) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.6129 time to fit residues: 204.8817 Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 197 GLN E 197 GLN G 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.044423 restraints weight = 36589.595| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 4.24 r_work: 0.2562 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 11000 Z= 0.313 Angle : 0.721 9.424 14944 Z= 0.348 Chirality : 0.043 0.156 1648 Planarity : 0.004 0.034 2000 Dihedral : 3.700 13.340 1552 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.67 % Allowed : 13.82 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.22), residues: 1352 helix: 2.01 (0.26), residues: 368 sheet: -1.04 (0.25), residues: 352 loop : -0.33 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 154 TYR 0.011 0.001 TYR E 140 PHE 0.010 0.001 PHE G 136 TRP 0.006 0.001 TRP D 56 HIS 0.003 0.002 HIS H 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.31 (11000) covalent geometry : angle 0.72092 / 0.35 (14944) hydrogen bonds : bond 0.04987 / 3.35 ( 416) hydrogen bonds : angle 4.41928 / 3.06 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.296 Fit side-chains REVERT: A 39 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9146 (pp) REVERT: A 65 THR cc_start: 0.8926 (p) cc_final: 0.8493 (p) REVERT: A 70 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8669 (mm-30) REVERT: A 161 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9262 (mppt) REVERT: B 70 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8498 (mm-30) REVERT: B 140 TYR cc_start: 0.9485 (m-80) cc_final: 0.9237 (m-80) REVERT: B 161 LYS cc_start: 0.9357 (mppt) cc_final: 0.9134 (mmtm) REVERT: B 170 GLU cc_start: 0.8817 (tp30) cc_final: 0.8614 (tp30) REVERT: C 39 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9132 (pp) REVERT: C 65 THR cc_start: 0.8935 (p) cc_final: 0.8458 (p) REVERT: C 70 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8547 (mm-30) REVERT: C 128 GLU cc_start: 0.9512 (tt0) cc_final: 0.9063 (tm-30) REVERT: C 161 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9303 (mmtm) REVERT: D 70 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8517 (mm-30) REVERT: D 140 TYR cc_start: 0.9508 (m-80) cc_final: 0.9272 (m-80) REVERT: D 161 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9195 (mmmt) REVERT: E 65 THR cc_start: 0.8965 (p) cc_final: 0.8597 (p) REVERT: E 70 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8539 (mp0) REVERT: E 161 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9304 (mmtm) REVERT: F 70 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8526 (mm-30) REVERT: F 132 ASP cc_start: 0.8900 (m-30) cc_final: 0.8651 (m-30) REVERT: F 140 TYR cc_start: 0.9512 (m-80) cc_final: 0.9255 (m-80) REVERT: F 161 LYS cc_start: 0.9436 (mmmm) cc_final: 0.9226 (mmmt) REVERT: F 189 LYS cc_start: 0.9750 (mmmm) cc_final: 0.9493 (mtmm) REVERT: G 65 THR cc_start: 0.8934 (p) cc_final: 0.8453 (p) REVERT: G 70 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8605 (mm-30) REVERT: G 128 GLU cc_start: 0.9513 (tt0) cc_final: 0.9109 (tm-30) REVERT: G 194 LEU cc_start: 0.9868 (tt) cc_final: 0.9641 (tm) REVERT: H 70 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8537 (mm-30) REVERT: H 132 ASP cc_start: 0.8888 (m-30) cc_final: 0.8624 (m-30) REVERT: H 161 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9234 (mmmt) REVERT: H 170 GLU cc_start: 0.8802 (tp30) cc_final: 0.8590 (tp30) REVERT: H 189 LYS cc_start: 0.9749 (mmmm) cc_final: 0.9463 (mtmm) outliers start: 19 outliers final: 2 residues processed: 214 average time/residue: 0.5664 time to fit residues: 130.0768 Evaluate side-chains 150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain E residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3060 r_free = 0.3060 target = 0.055536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.045178 restraints weight = 36648.887| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.24 r_work: 0.2603 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11000 Z= 0.186 Angle : 0.630 8.850 14944 Z= 0.308 Chirality : 0.041 0.147 1648 Planarity : 0.004 0.033 2000 Dihedral : 3.504 11.691 1552 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.02 % Allowed : 15.40 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1352 helix: 2.93 (0.24), residues: 368 sheet: -0.83 (0.25), residues: 352 loop : -0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 90 TYR 0.012 0.001 TYR C 140 PHE 0.004 0.001 PHE E 136 TRP 0.005 0.001 TRP D 91 HIS 0.002 0.001 HIS F 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (11000) covalent geometry : angle 0.62970 / 0.31 (14944) hydrogen bonds : bond 0.04651 / 3.11 ( 416) hydrogen bonds : angle 4.08634 / 2.85 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9131 (pp) REVERT: A 70 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8620 (mp0) REVERT: A 189 LYS cc_start: 0.9679 (mmmm) cc_final: 0.9383 (mtmm) REVERT: B 70 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8542 (mm-30) REVERT: B 132 ASP cc_start: 0.8869 (m-30) cc_final: 0.8625 (m-30) REVERT: B 139 GLU cc_start: 0.8693 (tp30) cc_final: 0.8456 (tp30) REVERT: B 140 TYR cc_start: 0.9511 (m-80) cc_final: 0.9274 (m-80) REVERT: B 161 LYS cc_start: 0.9357 (mppt) cc_final: 0.9155 (mppt) REVERT: B 179 LYS cc_start: 0.9046 (mppt) cc_final: 0.8820 (mppt) REVERT: C 39 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9123 (pp) REVERT: C 70 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8647 (mm-30) REVERT: C 128 GLU cc_start: 0.9508 (tt0) cc_final: 0.9156 (tm-30) REVERT: C 161 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9272 (mppt) REVERT: D 70 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8559 (mm-30) REVERT: D 139 GLU cc_start: 0.8682 (tp30) cc_final: 0.8424 (tp30) REVERT: D 140 TYR cc_start: 0.9522 (m-80) cc_final: 0.9301 (m-80) REVERT: E 70 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8595 (mp0) REVERT: E 161 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9271 (mppt) REVERT: E 179 LYS cc_start: 0.9214 (mppt) cc_final: 0.8966 (mppt) REVERT: E 189 LYS cc_start: 0.9487 (mtmp) cc_final: 0.9278 (mtmm) REVERT: F 70 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8506 (mm-30) REVERT: F 132 ASP cc_start: 0.8824 (m-30) cc_final: 0.8589 (m-30) REVERT: F 139 GLU cc_start: 0.8712 (tp30) cc_final: 0.8472 (tp30) REVERT: F 140 TYR cc_start: 0.9519 (m-80) cc_final: 0.9268 (m-80) REVERT: F 179 LYS cc_start: 0.9094 (mppt) cc_final: 0.8889 (mppt) REVERT: G 70 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8575 (mp0) REVERT: G 128 GLU cc_start: 0.9500 (tt0) cc_final: 0.9155 (tm-30) REVERT: G 161 LYS cc_start: 0.9511 (mmmm) cc_final: 0.9290 (mmtm) REVERT: G 189 LYS cc_start: 0.9678 (mmmm) cc_final: 0.9413 (mtmm) REVERT: H 70 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8507 (mm-30) REVERT: H 132 ASP cc_start: 0.8758 (m-30) cc_final: 0.8482 (m-30) REVERT: H 139 GLU cc_start: 0.8675 (tp30) cc_final: 0.8446 (tp30) REVERT: H 161 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9199 (mppt) REVERT: H 179 LYS cc_start: 0.9080 (mppt) cc_final: 0.8878 (mppt) outliers start: 23 outliers final: 4 residues processed: 199 average time/residue: 0.4560 time to fit residues: 98.7744 Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 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 = 0.3044 r_free = 0.3044 target = 0.054973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.044469 restraints weight = 37558.294| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.27 r_work: 0.2582 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11000 Z= 0.232 Angle : 0.638 8.827 14944 Z= 0.310 Chirality : 0.041 0.197 1648 Planarity : 0.004 0.031 2000 Dihedral : 3.525 11.174 1552 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.38 % Allowed : 15.05 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1352 helix: 3.19 (0.24), residues: 368 sheet: -1.09 (0.25), residues: 336 loop : -0.15 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.008 0.001 TYR G 140 PHE 0.005 0.001 PHE C 136 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (11000) covalent geometry : angle 0.63785 / 0.31 (14944) hydrogen bonds : bond 0.04761 / 3.19 ( 416) hydrogen bonds : angle 4.13046 / 2.88 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.366 Fit side-chains REVERT: A 39 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 65 THR cc_start: 0.9058 (p) cc_final: 0.8706 (p) REVERT: A 70 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8599 (mp0) REVERT: A 189 LYS cc_start: 0.9686 (mmmm) cc_final: 0.9407 (mtmm) REVERT: B 39 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9090 (pp) REVERT: B 65 THR cc_start: 0.8960 (p) cc_final: 0.8457 (p) REVERT: B 70 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8487 (mm-30) REVERT: B 139 GLU cc_start: 0.8644 (tp30) cc_final: 0.8325 (tp30) REVERT: B 140 TYR cc_start: 0.9511 (m-80) cc_final: 0.9280 (m-80) REVERT: B 161 LYS cc_start: 0.9374 (mppt) cc_final: 0.9114 (mmtm) REVERT: C 39 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9129 (pp) REVERT: C 65 THR cc_start: 0.9004 (p) cc_final: 0.8640 (p) REVERT: C 70 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8560 (mp0) REVERT: C 128 GLU cc_start: 0.9522 (tt0) cc_final: 0.9142 (tm-30) REVERT: C 161 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9225 (mmtm) REVERT: C 189 LYS cc_start: 0.9686 (mmmm) cc_final: 0.9423 (mtmm) REVERT: D 70 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8575 (mm-30) REVERT: D 161 LYS cc_start: 0.9291 (mppt) cc_final: 0.9027 (mmtm) REVERT: D 189 LYS cc_start: 0.9477 (mtmp) cc_final: 0.8881 (mtmm) REVERT: E 65 THR cc_start: 0.9041 (p) cc_final: 0.8671 (p) REVERT: E 70 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8549 (mp0) REVERT: E 161 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9213 (mmtm) REVERT: E 189 LYS cc_start: 0.9506 (mtmp) cc_final: 0.9286 (mtmm) REVERT: F 65 THR cc_start: 0.8934 (p) cc_final: 0.8482 (p) REVERT: F 70 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8511 (mm-30) REVERT: F 132 ASP cc_start: 0.8857 (m-30) cc_final: 0.8613 (m-30) REVERT: F 139 GLU cc_start: 0.8673 (tp30) cc_final: 0.8298 (tp30) REVERT: F 140 TYR cc_start: 0.9520 (m-80) cc_final: 0.9267 (m-80) REVERT: G 65 THR cc_start: 0.9024 (p) cc_final: 0.8656 (p) REVERT: G 70 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8541 (mp0) REVERT: G 128 GLU cc_start: 0.9514 (tt0) cc_final: 0.9137 (tm-30) REVERT: G 161 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9299 (mppt) REVERT: G 189 LYS cc_start: 0.9685 (mmmm) cc_final: 0.9414 (mtmm) REVERT: H 70 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8572 (mm-30) REVERT: H 132 ASP cc_start: 0.8829 (m-30) cc_final: 0.8572 (m-30) REVERT: H 139 GLU cc_start: 0.8677 (tp30) cc_final: 0.8361 (tp30) REVERT: H 161 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9186 (mmtm) REVERT: H 189 LYS cc_start: 0.9563 (mtmm) cc_final: 0.9338 (mtmm) outliers start: 27 outliers final: 6 residues processed: 192 average time/residue: 0.4431 time to fit residues: 92.5433 Evaluate side-chains 163 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** G 105 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 = 0.3053 r_free = 0.3053 target = 0.055027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.044183 restraints weight = 37104.065| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 4.40 r_work: 0.2586 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11000 Z= 0.224 Angle : 0.645 9.126 14944 Z= 0.312 Chirality : 0.041 0.157 1648 Planarity : 0.004 0.032 2000 Dihedral : 3.587 12.808 1552 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 15.05 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1352 helix: 3.48 (0.24), residues: 368 sheet: -0.71 (0.25), residues: 352 loop : -0.02 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 90 TYR 0.007 0.001 TYR G 140 PHE 0.005 0.001 PHE G 136 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (11000) covalent geometry : angle 0.64453 / 0.31 (14944) hydrogen bonds : bond 0.04675 / 3.13 ( 416) hydrogen bonds : angle 4.11470 / 2.88 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.454 Fit side-chains REVERT: A 39 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9117 (pp) REVERT: A 65 THR cc_start: 0.9072 (p) cc_final: 0.8647 (p) REVERT: A 70 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8597 (mp0) REVERT: A 161 LYS cc_start: 0.9376 (mppt) cc_final: 0.9122 (mmtm) REVERT: A 189 LYS cc_start: 0.9711 (mmmm) cc_final: 0.9448 (mtmm) REVERT: B 39 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9118 (pp) REVERT: B 65 THR cc_start: 0.9047 (p) cc_final: 0.8645 (t) REVERT: B 70 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8631 (mm-30) REVERT: B 139 GLU cc_start: 0.8632 (tp30) cc_final: 0.8287 (tp30) REVERT: B 140 TYR cc_start: 0.9499 (m-80) cc_final: 0.9260 (m-80) REVERT: B 161 LYS cc_start: 0.9416 (mppt) cc_final: 0.9214 (mmtm) REVERT: B 179 LYS cc_start: 0.9104 (mppt) cc_final: 0.8874 (mppt) REVERT: B 189 LYS cc_start: 0.9463 (mtmm) cc_final: 0.8987 (mtmm) REVERT: C 39 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9109 (pp) REVERT: C 65 THR cc_start: 0.9046 (p) cc_final: 0.8697 (p) REVERT: C 70 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8586 (mp0) REVERT: C 128 GLU cc_start: 0.9527 (tt0) cc_final: 0.9171 (tm-30) REVERT: C 189 LYS cc_start: 0.9708 (mmmm) cc_final: 0.9471 (mtmm) REVERT: D 65 THR cc_start: 0.8892 (p) cc_final: 0.8466 (p) REVERT: D 70 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8594 (mm-30) REVERT: D 132 ASP cc_start: 0.8839 (m-30) cc_final: 0.8639 (m-30) REVERT: D 140 TYR cc_start: 0.9407 (m-80) cc_final: 0.9113 (m-80) REVERT: D 189 LYS cc_start: 0.9513 (mtmp) cc_final: 0.9274 (mtmm) REVERT: D 209 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.9100 (tm-30) REVERT: E 65 THR cc_start: 0.9080 (p) cc_final: 0.8652 (p) REVERT: E 70 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8609 (mp0) REVERT: E 189 LYS cc_start: 0.9514 (mtmp) cc_final: 0.9282 (mtmm) REVERT: F 65 THR cc_start: 0.8960 (p) cc_final: 0.8530 (p) REVERT: F 70 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8614 (mm-30) REVERT: F 132 ASP cc_start: 0.8828 (m-30) cc_final: 0.8580 (m-30) REVERT: F 179 LYS cc_start: 0.9148 (mppt) cc_final: 0.8921 (mppt) REVERT: G 65 THR cc_start: 0.9039 (p) cc_final: 0.8684 (p) REVERT: G 70 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8586 (mp0) REVERT: G 128 GLU cc_start: 0.9528 (tt0) cc_final: 0.9170 (tm-30) REVERT: G 189 LYS cc_start: 0.9706 (mmmm) cc_final: 0.9468 (mtmm) REVERT: H 65 THR cc_start: 0.8968 (p) cc_final: 0.8564 (p) REVERT: H 70 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8591 (mm-30) REVERT: H 132 ASP cc_start: 0.8786 (m-30) cc_final: 0.8535 (m-30) REVERT: H 139 GLU cc_start: 0.8667 (tp30) cc_final: 0.8293 (tp30) REVERT: H 179 LYS cc_start: 0.9116 (mppt) cc_final: 0.8885 (mppt) outliers start: 30 outliers final: 8 residues processed: 195 average time/residue: 0.4510 time to fit residues: 95.7134 Evaluate side-chains 168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3061 r_free = 0.3061 target = 0.055025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.044150 restraints weight = 37110.704| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.39 r_work: 0.2600 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11000 Z= 0.211 Angle : 0.653 8.667 14944 Z= 0.313 Chirality : 0.041 0.219 1648 Planarity : 0.004 0.032 2000 Dihedral : 3.543 13.226 1552 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.55 % Allowed : 16.20 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1352 helix: 3.58 (0.23), residues: 368 sheet: -0.70 (0.25), residues: 352 loop : 0.05 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 90 TYR 0.008 0.001 TYR G 140 PHE 0.005 0.001 PHE C 136 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS F 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (11000) covalent geometry : angle 0.65326 / 0.31 (14944) hydrogen bonds : bond 0.04630 / 3.11 ( 416) hydrogen bonds : angle 4.13941 / 2.89 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.345 Fit side-chains REVERT: A 39 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9110 (pp) REVERT: A 65 THR cc_start: 0.9083 (p) cc_final: 0.8647 (p) REVERT: A 70 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8603 (mp0) REVERT: A 179 LYS cc_start: 0.9028 (mppt) cc_final: 0.8790 (mppt) REVERT: A 189 LYS cc_start: 0.9708 (mmmm) cc_final: 0.9447 (mtmm) REVERT: B 65 THR cc_start: 0.9053 (p) cc_final: 0.8607 (t) REVERT: B 70 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8594 (mm-30) REVERT: B 161 LYS cc_start: 0.9413 (mppt) cc_final: 0.9197 (mppt) REVERT: B 179 LYS cc_start: 0.9121 (mppt) cc_final: 0.8886 (mppt) REVERT: C 39 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9081 (pp) REVERT: C 65 THR cc_start: 0.9041 (p) cc_final: 0.8600 (p) REVERT: C 70 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8574 (mp0) REVERT: C 128 GLU cc_start: 0.9519 (tt0) cc_final: 0.9193 (tm-30) REVERT: C 161 LYS cc_start: 0.9398 (mppt) cc_final: 0.9185 (mmtm) REVERT: C 189 LYS cc_start: 0.9710 (mmmm) cc_final: 0.9472 (mtmm) REVERT: D 65 THR cc_start: 0.8890 (p) cc_final: 0.8475 (p) REVERT: D 70 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8569 (mm-30) REVERT: D 132 ASP cc_start: 0.8784 (m-30) cc_final: 0.8548 (m-30) REVERT: D 140 TYR cc_start: 0.9429 (m-80) cc_final: 0.9138 (m-80) REVERT: D 161 LYS cc_start: 0.9289 (mppt) cc_final: 0.9060 (mmtm) REVERT: D 189 LYS cc_start: 0.9514 (mtmp) cc_final: 0.9257 (mtmm) REVERT: D 209 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9077 (tm-30) REVERT: E 65 THR cc_start: 0.9104 (p) cc_final: 0.8670 (p) REVERT: E 70 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8613 (mp0) REVERT: E 161 LYS cc_start: 0.9397 (mppt) cc_final: 0.9172 (mmtm) REVERT: E 189 LYS cc_start: 0.9515 (mtmp) cc_final: 0.9269 (mtmm) REVERT: F 65 THR cc_start: 0.8936 (p) cc_final: 0.8526 (p) REVERT: F 70 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8581 (mm-30) REVERT: F 140 TYR cc_start: 0.9378 (m-80) cc_final: 0.9085 (m-80) REVERT: F 179 LYS cc_start: 0.9157 (mppt) cc_final: 0.8923 (mppt) REVERT: F 189 LYS cc_start: 0.9454 (mtmm) cc_final: 0.8983 (mtmm) REVERT: G 65 THR cc_start: 0.9024 (p) cc_final: 0.8578 (p) REVERT: G 70 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8584 (mp0) REVERT: G 128 GLU cc_start: 0.9505 (tt0) cc_final: 0.9182 (tm-30) REVERT: G 189 LYS cc_start: 0.9702 (mmmm) cc_final: 0.9466 (mtmm) REVERT: H 65 THR cc_start: 0.8935 (p) cc_final: 0.8532 (p) REVERT: H 70 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8570 (mm-30) REVERT: H 108 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8899 (mt0) REVERT: H 132 ASP cc_start: 0.8780 (m-30) cc_final: 0.8542 (m-30) REVERT: H 139 GLU cc_start: 0.8682 (tp30) cc_final: 0.8300 (tp30) REVERT: H 161 LYS cc_start: 0.9392 (mppt) cc_final: 0.9035 (mmtm) REVERT: H 179 LYS cc_start: 0.9126 (mppt) cc_final: 0.8887 (mppt) REVERT: H 189 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9316 (mtmm) outliers start: 29 outliers final: 8 residues processed: 191 average time/residue: 0.4071 time to fit residues: 84.8336 Evaluate side-chains 168 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain H residue 189 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3028 r_free = 0.3028 target = 0.053656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.043100 restraints weight = 37421.796| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 4.38 r_work: 0.2567 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11000 Z= 0.271 Angle : 0.697 10.225 14944 Z= 0.333 Chirality : 0.042 0.212 1648 Planarity : 0.004 0.032 2000 Dihedral : 3.667 14.663 1552 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.29 % Allowed : 16.64 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.22), residues: 1352 helix: 3.53 (0.24), residues: 368 sheet: -0.77 (0.24), residues: 352 loop : 0.04 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 90 TYR 0.010 0.001 TYR A 140 PHE 0.007 0.001 PHE C 136 TRP 0.007 0.001 TRP D 91 HIS 0.003 0.002 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.27 (11000) covalent geometry : angle 0.69693 / 0.33 (14944) hydrogen bonds : bond 0.04814 / 3.23 ( 416) hydrogen bonds : angle 4.22138 / 2.95 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.286 Fit side-chains REVERT: A 39 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9114 (pp) REVERT: A 65 THR cc_start: 0.9167 (p) cc_final: 0.8792 (p) REVERT: A 70 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8590 (mp0) REVERT: A 179 LYS cc_start: 0.9037 (mppt) cc_final: 0.8771 (mppt) REVERT: B 70 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8689 (mm-30) REVERT: B 161 LYS cc_start: 0.9409 (mppt) cc_final: 0.9175 (mppt) REVERT: B 179 LYS cc_start: 0.9159 (mppt) cc_final: 0.8908 (mppt) REVERT: C 39 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9099 (pp) REVERT: C 65 THR cc_start: 0.9133 (p) cc_final: 0.8742 (t) REVERT: C 70 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8618 (mp0) REVERT: C 128 GLU cc_start: 0.9545 (tt0) cc_final: 0.9200 (tm-30) REVERT: C 161 LYS cc_start: 0.9371 (mppt) cc_final: 0.9061 (mmtm) REVERT: D 65 THR cc_start: 0.8936 (p) cc_final: 0.8582 (t) REVERT: D 70 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8633 (mm-30) REVERT: D 140 TYR cc_start: 0.9493 (m-80) cc_final: 0.9156 (m-80) REVERT: D 189 LYS cc_start: 0.9523 (mtmp) cc_final: 0.9255 (mtmm) REVERT: E 65 THR cc_start: 0.9161 (p) cc_final: 0.8760 (p) REVERT: E 70 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8601 (mp0) REVERT: F 65 THR cc_start: 0.8985 (p) cc_final: 0.8548 (t) REVERT: F 70 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8599 (mp0) REVERT: F 132 ASP cc_start: 0.8910 (m-30) cc_final: 0.8696 (m-30) REVERT: F 140 TYR cc_start: 0.9449 (m-80) cc_final: 0.9198 (m-80) REVERT: F 179 LYS cc_start: 0.9187 (mppt) cc_final: 0.8952 (mppt) REVERT: F 189 LYS cc_start: 0.9467 (mtmm) cc_final: 0.8987 (mtmm) REVERT: G 65 THR cc_start: 0.9118 (p) cc_final: 0.8732 (t) REVERT: G 70 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8617 (mp0) REVERT: G 128 GLU cc_start: 0.9533 (tt0) cc_final: 0.9190 (tm-30) REVERT: H 65 THR cc_start: 0.8982 (p) cc_final: 0.8636 (t) REVERT: H 70 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8608 (mp0) REVERT: H 132 ASP cc_start: 0.8905 (m-30) cc_final: 0.8661 (m-30) REVERT: H 139 GLU cc_start: 0.8668 (tp30) cc_final: 0.8272 (tp30) REVERT: H 161 LYS cc_start: 0.9364 (mppt) cc_final: 0.9154 (mmtm) REVERT: H 179 LYS cc_start: 0.9165 (mppt) cc_final: 0.8913 (mppt) outliers start: 26 outliers final: 12 residues processed: 182 average time/residue: 0.3990 time to fit residues: 79.7688 Evaluate side-chains 171 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3049 r_free = 0.3049 target = 0.054708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043727 restraints weight = 37661.886| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 4.45 r_work: 0.2594 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11000 Z= 0.226 Angle : 0.707 10.623 14944 Z= 0.337 Chirality : 0.042 0.271 1648 Planarity : 0.004 0.033 2000 Dihedral : 3.631 14.303 1552 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.11 % Allowed : 17.25 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1352 helix: 3.51 (0.23), residues: 368 sheet: -0.84 (0.24), residues: 352 loop : 0.11 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 90 TYR 0.009 0.001 TYR G 140 PHE 0.006 0.001 PHE C 136 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (11000) covalent geometry : angle 0.70695 / 0.34 (14944) hydrogen bonds : bond 0.04694 / 3.14 ( 416) hydrogen bonds : angle 4.24758 / 2.98 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9079 (pp) REVERT: A 65 THR cc_start: 0.9166 (p) cc_final: 0.8717 (p) REVERT: A 70 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8617 (mp0) REVERT: A 179 LYS cc_start: 0.9023 (mppt) cc_final: 0.8773 (mppt) REVERT: B 161 LYS cc_start: 0.9430 (mppt) cc_final: 0.9211 (mppt) REVERT: B 179 LYS cc_start: 0.9155 (mppt) cc_final: 0.8918 (mppt) REVERT: C 39 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9065 (pp) REVERT: C 65 THR cc_start: 0.9111 (p) cc_final: 0.8672 (p) REVERT: C 70 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8562 (mp0) REVERT: C 128 GLU cc_start: 0.9528 (tt0) cc_final: 0.9189 (tm-30) REVERT: D 65 THR cc_start: 0.8931 (p) cc_final: 0.8579 (t) REVERT: D 70 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8651 (mm-30) REVERT: D 140 TYR cc_start: 0.9480 (m-80) cc_final: 0.9109 (m-80) REVERT: E 65 THR cc_start: 0.9140 (p) cc_final: 0.8673 (p) REVERT: E 70 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8592 (mp0) REVERT: F 65 THR cc_start: 0.8986 (p) cc_final: 0.8580 (t) REVERT: F 70 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8630 (mp0) REVERT: F 132 ASP cc_start: 0.8878 (m-30) cc_final: 0.8653 (m-30) REVERT: F 140 TYR cc_start: 0.9451 (m-80) cc_final: 0.9164 (m-80) REVERT: F 179 LYS cc_start: 0.9161 (mppt) cc_final: 0.8928 (mppt) REVERT: G 65 THR cc_start: 0.9092 (p) cc_final: 0.8645 (p) REVERT: G 70 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8573 (mp0) REVERT: G 128 GLU cc_start: 0.9536 (tt0) cc_final: 0.9192 (tm-30) REVERT: H 65 THR cc_start: 0.8992 (p) cc_final: 0.8586 (t) REVERT: H 70 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8595 (mp0) REVERT: H 132 ASP cc_start: 0.8771 (m-30) cc_final: 0.8542 (m-30) REVERT: H 139 GLU cc_start: 0.8663 (tp30) cc_final: 0.8234 (tp30) REVERT: H 179 LYS cc_start: 0.9155 (mppt) cc_final: 0.8915 (mppt) outliers start: 24 outliers final: 12 residues processed: 175 average time/residue: 0.4442 time to fit residues: 84.9996 Evaluate side-chains 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3037 r_free = 0.3037 target = 0.054472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.043590 restraints weight = 37146.738| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.39 r_work: 0.2575 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11000 Z= 0.248 Angle : 0.740 11.180 14944 Z= 0.352 Chirality : 0.043 0.299 1648 Planarity : 0.004 0.033 2000 Dihedral : 3.703 14.667 1552 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.02 % Allowed : 17.25 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1352 helix: 3.35 (0.23), residues: 368 sheet: -0.94 (0.24), residues: 352 loop : 0.16 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 90 TYR 0.010 0.001 TYR C 140 PHE 0.006 0.001 PHE C 136 TRP 0.006 0.001 TRP D 91 HIS 0.002 0.001 HIS E 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (11000) covalent geometry : angle 0.74015 / 0.35 (14944) hydrogen bonds : bond 0.04754 / 3.18 ( 416) hydrogen bonds : angle 4.29204 / 3.01 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9105 (pp) REVERT: A 65 THR cc_start: 0.9157 (p) cc_final: 0.8770 (p) REVERT: A 70 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8610 (mp0) REVERT: A 179 LYS cc_start: 0.9059 (mppt) cc_final: 0.8833 (mppt) REVERT: B 161 LYS cc_start: 0.9429 (mppt) cc_final: 0.9201 (mppt) REVERT: B 179 LYS cc_start: 0.9160 (mppt) cc_final: 0.8899 (mppt) REVERT: C 39 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9076 (pp) REVERT: C 65 THR cc_start: 0.9107 (p) cc_final: 0.8653 (t) REVERT: C 70 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8602 (mp0) REVERT: C 128 GLU cc_start: 0.9529 (tt0) cc_final: 0.9205 (tm-30) REVERT: D 65 THR cc_start: 0.8934 (p) cc_final: 0.8579 (t) REVERT: D 70 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8629 (mm-30) REVERT: D 140 TYR cc_start: 0.9493 (m-80) cc_final: 0.9091 (m-80) REVERT: D 189 LYS cc_start: 0.9527 (mtmp) cc_final: 0.9243 (mtmm) REVERT: E 65 THR cc_start: 0.9164 (p) cc_final: 0.8762 (p) REVERT: E 70 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8599 (mp0) REVERT: F 65 THR cc_start: 0.8969 (p) cc_final: 0.8552 (t) REVERT: F 70 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8638 (mp0) REVERT: F 128 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8918 (tp30) REVERT: F 132 ASP cc_start: 0.8940 (m-30) cc_final: 0.8711 (m-30) REVERT: F 140 TYR cc_start: 0.9469 (m-80) cc_final: 0.9152 (m-80) REVERT: F 179 LYS cc_start: 0.9176 (mppt) cc_final: 0.8916 (mppt) REVERT: G 65 THR cc_start: 0.9103 (p) cc_final: 0.8649 (t) REVERT: G 70 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8602 (mp0) REVERT: G 128 GLU cc_start: 0.9517 (tt0) cc_final: 0.9196 (tm-30) REVERT: H 65 THR cc_start: 0.8984 (p) cc_final: 0.8594 (t) REVERT: H 70 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8601 (mp0) REVERT: H 108 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8934 (mt0) REVERT: H 128 GLU cc_start: 0.9304 (tm-30) cc_final: 0.9023 (tp30) REVERT: H 132 ASP cc_start: 0.8875 (m-30) cc_final: 0.8638 (m-30) REVERT: H 139 GLU cc_start: 0.8640 (tp30) cc_final: 0.8223 (tp30) REVERT: H 179 LYS cc_start: 0.9172 (mppt) cc_final: 0.8911 (mppt) outliers start: 23 outliers final: 13 residues processed: 175 average time/residue: 0.4475 time to fit residues: 85.4161 Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 108 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN C 105 GLN E 105 GLN F 209 GLN G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044822 restraints weight = 36701.947| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.49 r_work: 0.2625 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11000 Z= 0.149 Angle : 0.707 10.478 14944 Z= 0.339 Chirality : 0.043 0.297 1648 Planarity : 0.003 0.036 2000 Dihedral : 3.551 13.522 1552 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.23 % Allowed : 17.87 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.22), residues: 1352 helix: 3.49 (0.23), residues: 368 sheet: -0.89 (0.25), residues: 352 loop : 0.28 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 90 TYR 0.009 0.001 TYR B 151 PHE 0.005 0.001 PHE H 107 TRP 0.005 0.001 TRP D 91 HIS 0.001 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11000) covalent geometry : angle 0.70717 / 0.34 (14944) hydrogen bonds : bond 0.04368 / 2.91 ( 416) hydrogen bonds : angle 4.20721 / 2.94 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9108 (pp) REVERT: A 70 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8635 (mp0) REVERT: A 128 GLU cc_start: 0.8841 (tp30) cc_final: 0.8558 (tp30) REVERT: A 179 LYS cc_start: 0.9055 (mppt) cc_final: 0.8851 (mppt) REVERT: B 161 LYS cc_start: 0.9431 (mppt) cc_final: 0.9040 (mmtm) REVERT: B 179 LYS cc_start: 0.9111 (mppt) cc_final: 0.8844 (mppt) REVERT: C 39 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9081 (pp) REVERT: C 65 THR cc_start: 0.8924 (p) cc_final: 0.8436 (p) REVERT: C 70 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8539 (mp0) REVERT: C 128 GLU cc_start: 0.9494 (tt0) cc_final: 0.9193 (tm-30) REVERT: C 189 LYS cc_start: 0.9688 (mmmm) cc_final: 0.9485 (mtmp) REVERT: D 70 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8579 (mm-30) REVERT: D 140 TYR cc_start: 0.9458 (m-80) cc_final: 0.9062 (m-80) REVERT: D 189 LYS cc_start: 0.9526 (mtmp) cc_final: 0.9231 (mtmm) REVERT: E 70 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8623 (mp0) REVERT: E 128 GLU cc_start: 0.8874 (tp30) cc_final: 0.8549 (tp30) REVERT: F 70 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8573 (mp0) REVERT: F 128 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8839 (tp30) REVERT: F 140 TYR cc_start: 0.9400 (m-80) cc_final: 0.9048 (m-80) REVERT: F 179 LYS cc_start: 0.9144 (mppt) cc_final: 0.8877 (mppt) REVERT: F 209 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8930 (tm-30) REVERT: G 65 THR cc_start: 0.8916 (p) cc_final: 0.8433 (p) REVERT: G 70 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8540 (mp0) REVERT: G 128 GLU cc_start: 0.9500 (tt0) cc_final: 0.9182 (tm-30) REVERT: G 161 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9267 (mmpt) REVERT: H 70 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8616 (mp0) REVERT: H 108 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8887 (mt0) REVERT: H 128 GLU cc_start: 0.9214 (tm-30) cc_final: 0.9014 (tp30) REVERT: H 132 ASP cc_start: 0.8688 (m-30) cc_final: 0.8426 (m-30) REVERT: H 179 LYS cc_start: 0.9120 (mppt) cc_final: 0.8848 (mppt) outliers start: 14 outliers final: 5 residues processed: 179 average time/residue: 0.4295 time to fit residues: 83.8691 Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain H residue 108 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 132 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 0.0030 chunk 111 optimal weight: 9.9990 overall best weight: 4.9196 ------------------------------------------------------------------------------- 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 = 0.3079 r_free = 0.3079 target = 0.055941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.044994 restraints weight = 36711.447| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.44 r_work: 0.2630 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 11000 Z= 0.233 Angle : 0.973 59.188 14944 Z= 0.527 Chirality : 0.044 0.346 1648 Planarity : 0.004 0.046 2000 Dihedral : 3.550 12.853 1552 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.14 % Allowed : 17.96 % Favored : 80.90 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.22), residues: 1352 helix: 3.49 (0.23), residues: 368 sheet: -0.90 (0.25), residues: 352 loop : 0.27 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG H 77 TYR 0.005 0.001 TYR B 140 PHE 0.010 0.001 PHE E 136 TRP 0.005 0.001 TRP D 91 HIS 0.001 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (11000) covalent geometry : angle 0.97287 / 0.53 (14944) hydrogen bonds : bond 0.04393 / 2.93 ( 416) hydrogen bonds : angle 4.21604 / 2.95 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.25 seconds wall clock time: 47 minutes 32.87 seconds (2852.87 seconds total)