Starting phenix.real_space_refine on Wed Aug 5 02:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7m_72659/08_2026/9y7m_72659.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2526 2.51 5 N 711 2.21 5 O 825 1.98 5 H 3809 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7885 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3316 Classifications: {'peptide': 223} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "A" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1243 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 11, 'ASN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3326 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 7885 At special positions: 0 Unit cell: (59.44, 66.127, 122.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 825 8.00 N 711 7.00 C 2526 6.00 H 3809 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 199 " distance=2.04 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: 0.64 Conformation dependent library (CDL) restraints added in 311.5 milliseconds 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 17.4% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.933A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.660A pdb=" N VAL A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 176 through 184 removed outlier: 4.222A pdb=" N PHE A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.629A pdb=" N HIS C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 4.179A pdb=" N ALA B 33 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.642A pdb=" N CYS B 98 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP B 111 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 100 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.161A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.127A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 78 removed outlier: 5.521A pdb=" N VAL A 72 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS A 87 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 82 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.875A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 89 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 38 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR C 54 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP C 40 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.875A pdb=" N ASP C 110 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 89 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 102 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 119 through 123 removed outlier: 5.713A pdb=" N TYR C 178 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 160 removed outlier: 4.489A pdb=" N TRP C 153 " --> pdb=" O GLN C 160 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 531 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: 1.78 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3808 1.03 - 1.23: 14 1.23 - 1.42: 1785 1.42 - 1.62: 2346 1.62 - 1.81: 19 Bond restraints: 7972 Sorted by residual: bond pdb=" N LEU C 0 " pdb=" H1 LEU C 0 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLN B 1 " pdb=" H3 GLN B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLN B 1 " pdb=" CA GLN B 1 " ideal model delta sigma weight residual 1.491 1.458 0.033 2.10e-02 2.27e+03 2.50e+00 bond pdb=" N GLN B 1 " pdb=" H1 GLN B 1 " ideal model delta sigma weight residual 0.890 0.860 0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 7967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 14207 5.42 - 10.84: 1 10.84 - 16.27: 0 16.27 - 21.69: 1 21.69 - 27.11: 1 Bond angle restraints: 14210 Sorted by residual: angle pdb=" H1 GLN B 1 " pdb=" N GLN B 1 " pdb=" H2 GLN B 1 " ideal model delta sigma weight residual 109.47 82.36 27.11 3.00e+00 1.11e-01 8.17e+01 angle pdb=" H1 GLN B 1 " pdb=" N GLN B 1 " pdb=" H3 GLN B 1 " ideal model delta sigma weight residual 109.47 127.46 -17.99 3.00e+00 1.11e-01 3.60e+01 angle pdb=" CB GLU C 192 " pdb=" CG GLU C 192 " pdb=" CD GLU C 192 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.70e+00 3.46e-01 4.50e+00 angle pdb=" CA GLU B 220 " pdb=" CB GLU B 220 " pdb=" CG GLU B 220 " ideal model delta sigma weight residual 114.10 118.23 -4.13 2.00e+00 2.50e-01 4.27e+00 angle pdb=" CB GLU B 220 " pdb=" CG GLU B 220 " pdb=" CD GLU B 220 " ideal model delta sigma weight residual 112.60 116.01 -3.41 1.70e+00 3.46e-01 4.02e+00 ... (remaining 14205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3413 17.97 - 35.95: 238 35.95 - 53.92: 72 53.92 - 71.90: 18 71.90 - 89.87: 7 Dihedral angle restraints: 3748 sinusoidal: 2010 harmonic: 1738 Sorted by residual: dihedral pdb=" CA PRO A 117 " pdb=" C PRO A 117 " pdb=" N ASP A 118 " pdb=" CA ASP A 118 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASN B 163 " pdb=" C ASN B 163 " pdb=" N SER B 164 " pdb=" CA SER B 164 " ideal model delta harmonic sigma weight residual 180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 93 " pdb=" CB CYS C 93 " ideal model delta sinusoidal sigma weight residual 93.00 65.17 27.83 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 3745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 315 0.027 - 0.053: 176 0.053 - 0.080: 27 0.080 - 0.107: 35 0.107 - 0.133: 23 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA VAL B 192 " pdb=" N VAL B 192 " pdb=" C VAL B 192 " pdb=" CB VAL B 192 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL C 63 " pdb=" N VAL C 63 " pdb=" C VAL C 63 " pdb=" CB VAL C 63 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 573 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 192 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 193 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 210 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 13 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO B 14 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.014 5.00e-02 4.00e+02 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.43: 3697 2.43 - 2.97: 17036 2.97 - 3.51: 18442 3.51 - 4.06: 25794 4.06 - 4.60: 36929 Nonbonded interactions: 101898 Sorted by model distance: nonbonded pdb=" H GLN B 6 " pdb="HE22 GLN B 113 " model vdw 1.882 2.100 nonbonded pdb=" HD1 TYR B 103 " pdb=" HD2 TYR B 104 " model vdw 1.887 2.100 nonbonded pdb=" HB2 GLN C 152 " pdb="HE21 GLN C 152 " model vdw 1.912 2.270 nonbonded pdb=" H THR B 168 " pdb=" H SER B 169 " model vdw 1.914 2.100 nonbonded pdb=" H PHE C 67 " pdb=" HD1 PHE C 67 " model vdw 1.925 2.100 ... (remaining 101893 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4167 Z= 0.125 Angle : 0.511 4.577 5628 Z= 0.267 Chirality : 0.043 0.133 576 Planarity : 0.003 0.033 754 Dihedral : 13.127 86.385 1452 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.92 % Allowed : 14.66 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.15 (0.37), residues: 572 helix: 2.37 (0.68), residues: 64 sheet: 0.16 (0.34), residues: 247 loop : -0.46 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.015 0.001 TYR B 104 PHE 0.006 0.001 PHE B 174 TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 4163) covalent geometry : angle 0.51000 / 0.27 ( 5620) SS BOND : bond 0.00444 / 0.22 ( 4) SS BOND : angle 0.79656 / 0.60 ( 8) hydrogen bonds : bond 0.23730 / 15.99 ( 198) hydrogen bonds : angle 9.37138 / 6.35 ( 531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6818 (mmtp) cc_final: 0.6485 (mtmt) REVERT: B 216 ASP cc_start: 0.7764 (m-30) cc_final: 0.7305 (t0) REVERT: C 84 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7051 (mm-30) REVERT: C 174 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8024 (tmmm) REVERT: C 195 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8247 (tppt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.8352 time to fit residues: 41.1181 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 25 optimal weight: 40.0000 chunk 50 optimal weight: 0.3980 overall best weight: 1.0322 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079424 restraints weight = 19519.379| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.03 r_work: 0.3200 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4167 Z= 0.177 Angle : 0.567 5.222 5628 Z= 0.296 Chirality : 0.045 0.135 576 Planarity : 0.004 0.035 754 Dihedral : 5.249 35.757 631 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.44 % Allowed : 14.90 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.44 (0.38), residues: 572 helix: 2.63 (0.68), residues: 65 sheet: 0.38 (0.34), residues: 246 loop : -0.31 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.014 0.001 TYR B 104 PHE 0.011 0.002 PHE C 103 TRP 0.017 0.002 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 4163) covalent geometry : angle 0.56640 / 0.30 ( 5620) SS BOND : bond 0.00695 / 0.35 ( 4) SS BOND : angle 1.07694 / 0.82 ( 8) hydrogen bonds : bond 0.03670 / 2.38 ( 198) hydrogen bonds : angle 6.54369 / 4.45 ( 531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6867 (mmtp) cc_final: 0.6512 (mtmt) REVERT: B 75 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7732 (t70) REVERT: B 216 ASP cc_start: 0.7485 (m-30) cc_final: 0.7116 (t0) REVERT: C 84 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7142 (mm-30) REVERT: C 174 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8092 (tmmm) REVERT: C 195 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8215 (tppt) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.8902 time to fit residues: 42.9776 Evaluate side-chains 46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.109903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079947 restraints weight = 19232.914| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.00 r_work: 0.3224 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4167 Z= 0.120 Angle : 0.520 4.240 5628 Z= 0.269 Chirality : 0.044 0.136 576 Planarity : 0.003 0.033 754 Dihedral : 4.664 34.940 626 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.40 % Allowed : 13.94 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.58 (0.38), residues: 572 helix: 2.82 (0.68), residues: 65 sheet: 0.53 (0.34), residues: 244 loop : -0.31 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 59 TYR 0.017 0.001 TYR B 104 PHE 0.009 0.001 PHE B 50 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4163) covalent geometry : angle 0.51879 / 0.27 ( 5620) SS BOND : bond 0.00581 / 0.29 ( 4) SS BOND : angle 0.92537 / 0.73 ( 8) hydrogen bonds : bond 0.03075 / 1.98 ( 198) hydrogen bonds : angle 5.83359 / 3.96 ( 531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6593 (mmtp) cc_final: 0.6211 (mtmt) REVERT: B 216 ASP cc_start: 0.7458 (m-30) cc_final: 0.7130 (t0) REVERT: C 84 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7064 (mm-30) REVERT: C 174 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8099 (tmmm) REVERT: C 195 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8333 (tppt) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.9268 time to fit residues: 48.4186 Evaluate side-chains 51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.4540 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.111032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081066 restraints weight = 19438.324| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.08 r_work: 0.3220 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4167 Z= 0.102 Angle : 0.505 4.210 5628 Z= 0.260 Chirality : 0.043 0.136 576 Planarity : 0.003 0.035 754 Dihedral : 4.547 34.838 626 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.40 % Allowed : 13.94 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.38), residues: 572 helix: 2.97 (0.68), residues: 65 sheet: 0.63 (0.34), residues: 244 loop : -0.23 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 98 TYR 0.015 0.001 TYR B 104 PHE 0.012 0.001 PHE A 93 TRP 0.013 0.001 TRP B 162 HIS 0.001 0.000 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 ( 4163) covalent geometry : angle 0.50457 / 0.26 ( 5620) SS BOND : bond 0.00531 / 0.26 ( 4) SS BOND : angle 0.84778 / 0.67 ( 8) hydrogen bonds : bond 0.02704 / 1.75 ( 198) hydrogen bonds : angle 5.48026 / 3.72 ( 531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6620 (mmtp) cc_final: 0.6256 (mtmt) REVERT: B 216 ASP cc_start: 0.7525 (m-30) cc_final: 0.7133 (t0) REVERT: C 84 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7034 (mm-30) REVERT: C 172 ASP cc_start: 0.8731 (t70) cc_final: 0.8296 (t0) REVERT: C 174 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8139 (tmmm) REVERT: C 195 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8411 (tppt) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.8388 time to fit residues: 44.0963 Evaluate side-chains 47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079826 restraints weight = 19534.243| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.02 r_work: 0.3200 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4167 Z= 0.145 Angle : 0.540 5.449 5628 Z= 0.278 Chirality : 0.044 0.132 576 Planarity : 0.003 0.036 754 Dihedral : 4.600 34.592 626 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.40 % Allowed : 14.66 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.38), residues: 572 helix: 2.92 (0.67), residues: 65 sheet: 0.65 (0.34), residues: 244 loop : -0.29 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.013 0.001 TYR B 104 PHE 0.009 0.001 PHE B 50 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 4163) covalent geometry : angle 0.52997 / 0.27 ( 5620) SS BOND : bond 0.00574 / 0.28 ( 4) SS BOND : angle 2.74465 / 1.62 ( 8) hydrogen bonds : bond 0.02868 / 1.84 ( 198) hydrogen bonds : angle 5.45621 / 3.70 ( 531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6756 (mmtp) cc_final: 0.6439 (mtmt) REVERT: B 216 ASP cc_start: 0.7483 (m-30) cc_final: 0.7114 (t0) REVERT: C 84 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7061 (mm-30) REVERT: C 195 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8417 (tppt) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.8130 time to fit residues: 39.2989 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 50.0000 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.109273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078967 restraints weight = 19510.896| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.06 r_work: 0.3189 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4167 Z= 0.163 Angle : 0.546 4.832 5628 Z= 0.282 Chirality : 0.044 0.134 576 Planarity : 0.003 0.037 754 Dihedral : 4.511 27.890 622 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.92 % Allowed : 15.38 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.71 (0.38), residues: 572 helix: 2.94 (0.67), residues: 65 sheet: 0.65 (0.34), residues: 246 loop : -0.30 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.014 0.001 TYR B 104 PHE 0.009 0.001 PHE B 50 TRP 0.016 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 4163) covalent geometry : angle 0.54078 / 0.28 ( 5620) SS BOND : bond 0.00613 / 0.30 ( 4) SS BOND : angle 1.98380 / 1.22 ( 8) hydrogen bonds : bond 0.02887 / 1.86 ( 198) hydrogen bonds : angle 5.40792 / 3.68 ( 531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6823 (mmtp) cc_final: 0.6482 (mtmt) REVERT: B 216 ASP cc_start: 0.7487 (m-30) cc_final: 0.7141 (t0) REVERT: C 84 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7122 (mm-30) REVERT: C 172 ASP cc_start: 0.8794 (t70) cc_final: 0.8394 (t0) REVERT: C 195 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8353 (tppt) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.7604 time to fit residues: 37.7105 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 35 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.110542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080285 restraints weight = 19423.900| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.06 r_work: 0.3207 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4167 Z= 0.115 Angle : 0.521 4.832 5628 Z= 0.269 Chirality : 0.044 0.135 576 Planarity : 0.003 0.037 754 Dihedral : 4.404 28.556 622 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 15.62 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.81 (0.38), residues: 572 helix: 3.08 (0.67), residues: 65 sheet: 0.73 (0.34), residues: 244 loop : -0.25 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.013 0.001 TYR B 104 PHE 0.017 0.001 PHE A 93 TRP 0.015 0.001 TRP B 162 HIS 0.001 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 ( 4163) covalent geometry : angle 0.51772 / 0.27 ( 5620) SS BOND : bond 0.00550 / 0.27 ( 4) SS BOND : angle 1.51676 / 0.96 ( 8) hydrogen bonds : bond 0.02660 / 1.71 ( 198) hydrogen bonds : angle 5.17219 / 3.56 ( 531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6291 (mtmt) REVERT: B 216 ASP cc_start: 0.7469 (m-30) cc_final: 0.7122 (t0) REVERT: C 84 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7090 (mm-30) REVERT: C 195 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8362 (tppt) outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.7748 time to fit residues: 37.5471 Evaluate side-chains 48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.109458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079557 restraints weight = 19510.511| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.97 r_work: 0.3203 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4167 Z= 0.138 Angle : 0.529 4.721 5628 Z= 0.274 Chirality : 0.044 0.139 576 Planarity : 0.003 0.037 754 Dihedral : 4.406 28.959 622 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.92 % Allowed : 15.62 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.83 (0.38), residues: 572 helix: 3.01 (0.67), residues: 65 sheet: 0.78 (0.34), residues: 246 loop : -0.26 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 98 TYR 0.012 0.001 TYR B 104 PHE 0.017 0.002 PHE A 93 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4163) covalent geometry : angle 0.52587 / 0.27 ( 5620) SS BOND : bond 0.00572 / 0.28 ( 4) SS BOND : angle 1.51552 / 0.97 ( 8) hydrogen bonds : bond 0.02734 / 1.74 ( 198) hydrogen bonds : angle 5.15947 / 3.55 ( 531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6785 (mmtp) cc_final: 0.6431 (mtmt) REVERT: B 216 ASP cc_start: 0.7435 (m-30) cc_final: 0.7080 (t0) REVERT: C 84 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7086 (mm-30) REVERT: C 172 ASP cc_start: 0.8739 (t70) cc_final: 0.8301 (t0) REVERT: C 195 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8345 (tppt) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.7826 time to fit residues: 38.7344 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 30.0000 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.109667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079738 restraints weight = 19277.211| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.97 r_work: 0.3206 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4167 Z= 0.132 Angle : 0.535 4.700 5628 Z= 0.275 Chirality : 0.044 0.135 576 Planarity : 0.003 0.037 754 Dihedral : 4.375 29.283 622 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.92 % Allowed : 16.11 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.87 (0.38), residues: 572 helix: 3.04 (0.67), residues: 65 sheet: 0.81 (0.34), residues: 246 loop : -0.25 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 52 TYR 0.012 0.001 TYR B 104 PHE 0.008 0.001 PHE B 50 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 4163) covalent geometry : angle 0.53216 / 0.27 ( 5620) SS BOND : bond 0.00572 / 0.28 ( 4) SS BOND : angle 1.49681 / 1.00 ( 8) hydrogen bonds : bond 0.02677 / 1.72 ( 198) hydrogen bonds : angle 5.10234 / 3.52 ( 531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6666 (mmtp) cc_final: 0.6303 (mtmt) REVERT: B 216 ASP cc_start: 0.7428 (m-30) cc_final: 0.7075 (t0) REVERT: C 84 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7093 (mm-30) REVERT: C 195 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8366 (tppt) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.8013 time to fit residues: 38.8473 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.110253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080333 restraints weight = 19415.426| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.02 r_work: 0.3201 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4167 Z= 0.141 Angle : 0.541 4.685 5628 Z= 0.280 Chirality : 0.044 0.135 576 Planarity : 0.003 0.037 754 Dihedral : 4.390 29.636 622 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.92 % Allowed : 16.11 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.87 (0.38), residues: 572 helix: 3.05 (0.67), residues: 65 sheet: 0.82 (0.34), residues: 246 loop : -0.26 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 98 TYR 0.012 0.001 TYR B 104 PHE 0.019 0.002 PHE A 93 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4163) covalent geometry : angle 0.53841 / 0.28 ( 5620) SS BOND : bond 0.00600 / 0.30 ( 4) SS BOND : angle 1.55621 / 1.07 ( 8) hydrogen bonds : bond 0.02723 / 1.75 ( 198) hydrogen bonds : angle 5.09945 / 3.52 ( 531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1144 Ramachandran restraints generated. 572 Oldfield, 0 Emsley, 572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ALA 21 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue ILE 61 is missing expected H atoms. Skipping. Residue THR 66 is missing expected H atoms. Skipping. Residue ALA 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue ALA 74 is missing expected H atoms. Skipping. Residue MET 75 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue THR 89 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue SER 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue VAL 172 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue THR 188 is missing expected H atoms. Skipping. Residue ALA 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6832 (mmtp) cc_final: 0.6476 (mtmt) REVERT: B 216 ASP cc_start: 0.7445 (m-30) cc_final: 0.7111 (t0) REVERT: C 84 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7116 (mm-30) REVERT: C 172 ASP cc_start: 0.8773 (t70) cc_final: 0.8372 (t0) REVERT: C 195 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8414 (tppt) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.7863 time to fit residues: 38.9798 Evaluate side-chains 49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.109754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079921 restraints weight = 19421.815| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.94 r_work: 0.3194 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4167 Z= 0.157 Angle : 0.551 4.703 5628 Z= 0.285 Chirality : 0.044 0.135 576 Planarity : 0.003 0.037 754 Dihedral : 4.457 30.017 622 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.92 % Allowed : 16.11 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.86 (0.38), residues: 572 helix: 3.08 (0.67), residues: 65 sheet: 0.81 (0.34), residues: 246 loop : -0.28 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.013 0.001 TYR B 104 PHE 0.009 0.001 PHE B 50 TRP 0.015 0.001 TRP B 162 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 4163) covalent geometry : angle 0.54840 / 0.28 ( 5620) SS BOND : bond 0.00598 / 0.30 ( 4) SS BOND : angle 1.59379 / 1.08 ( 8) hydrogen bonds : bond 0.02788 / 1.79 ( 198) hydrogen bonds : angle 5.12754 / 3.54 ( 531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3579.24 seconds wall clock time: 61 minutes 19.50 seconds (3679.50 seconds total)