Starting phenix.real_space_refine on Wed Mar 4 05:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yc6_72761/03_2026/9yc6_72761.map" } resolution = 4.8 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= 0.001 sd= 0.019 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 48 5.16 5 C 3400 2.51 5 N 944 2.21 5 O 1123 1.98 5 H 5181 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10696 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3232 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "U" Number of atoms: 4194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4194 Classifications: {'peptide': 283} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain: "H" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3175 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N SER L 10 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER L 10 " occ=0.50 residue: pdb=" N SER L 20 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER L 20 " occ=0.50 residue: pdb=" N SER L 31 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER L 31 " occ=0.50 residue: pdb=" N SER L 127 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER L 127 " occ=0.50 residue: pdb=" N SER L 208 " occ=0.33 ... (9 atoms not shown) pdb=" HG SER L 208 " occ=0.33 residue: pdb=" N SER H 17 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER H 17 " occ=0.50 residue: pdb=" N GLY H 42 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY H 42 " occ=0.50 residue: pdb=" N GLY H 44 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY H 44 " occ=0.50 residue: pdb=" N ASP H 73 " occ=0.50 ... (10 atoms not shown) pdb=" HB3 ASP H 73 " occ=0.50 residue: pdb=" N SER H 75 " occ=0.50 ... (9 atoms not shown) pdb=" HG SER H 75 " occ=0.50 residue: pdb=" N VAL H 142 " occ=0.50 ... (14 atoms not shown) pdb="HG23 VAL H 142 " occ=0.50 residue: pdb=" N CYS H 146 " occ=0.33 ... (8 atoms not shown) pdb=" HB3 CYS H 146 " occ=0.33 ... (remaining 3 not shown) Time building chain proxies: 2.28, per 1000 atoms: 0.21 Number of scatterers: 10696 At special positions: 0 Unit cell: (68.25, 71.25, 130.5, 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 48 16.00 O 1123 8.00 N 944 7.00 C 3400 6.00 H 5181 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS U 3 " - pdb=" SG CYS U 24 " distance=2.03 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 12 " distance=2.04 Simple disulfide: pdb=" SG CYS U 17 " - pdb=" SG CYS U 45 " distance=2.03 Simple disulfide: pdb=" SG CYS U 47 " - pdb=" SG CYS U 259 " distance=2.02 Simple disulfide: pdb=" SG CYS U 71 " - pdb=" SG CYS U 76 " distance=2.02 Simple disulfide: pdb=" SG CYS U 95 " - pdb=" SG CYS U 122 " distance=2.01 Simple disulfide: pdb=" SG CYS U 98 " - pdb=" SG CYS U 105 " distance=2.01 Simple disulfide: pdb=" SG CYS U 115 " - pdb=" SG CYS U 147 " distance=2.04 Simple disulfide: pdb=" SG CYS U 153 " - pdb=" SG CYS U 170 " distance=2.02 Simple disulfide: pdb=" SG CYS U 171 " - pdb=" SG CYS U 176 " distance=2.02 Simple disulfide: pdb=" SG CYS U 194 " - pdb=" SG CYS U 222 " distance=2.02 Simple disulfide: pdb=" SG CYS U 197 " - pdb=" SG CYS U 205 " distance=2.04 Simple disulfide: pdb=" SG CYS U 215 " - pdb=" SG CYS U 241 " distance=2.03 Simple disulfide: pdb=" SG CYS U 247 " - pdb=" SG CYS U 265 " distance=2.01 Simple disulfide: pdb=" SG CYS U 266 " - pdb=" SG CYS U 271 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=1.98 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 1 " - " ASN U 200 " " NAG B 1 " - " ASN U 52 " " NAG U 301 " - " ASN U 172 " " NAG U 302 " - " ASN U 162 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 350.4 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 10 sheets defined 6.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.596A pdb=" N VAL L 83 " --> pdb=" O ILE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.546A pdb=" N SER L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'U' and resid 183 through 187 Processing helix chain 'U' and resid 252 through 257 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 159 through 164 removed outlier: 4.215A pdb=" N SER H 162 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 35 through 39 removed outlier: 3.823A pdb=" N SER L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 114 through 116 removed outlier: 5.987A pdb=" N SER L 173 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'U' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'U' and resid 23 through 33 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 36 through 46 current: chain 'U' and resid 66 through 71 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 66 through 71 current: chain 'U' and resid 111 through 114 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 111 through 114 current: chain 'U' and resid 164 through 171 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 164 through 171 current: chain 'U' and resid 211 through 216 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 211 through 216 current: chain 'U' and resid 237 through 242 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 60 removed outlier: 5.211A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 125 through 128 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 141 through 151 current: chain 'H' and resid 181 through 190 97 hydrogen bonds defined for protein. 225 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: 2.17 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 5177 1.12 - 1.30: 957 1.30 - 1.47: 2104 1.47 - 1.65: 2515 1.65 - 1.82: 58 Bond restraints: 10811 Sorted by residual: bond pdb=" CA GLN U 78 " pdb=" C GLN U 78 " ideal model delta sigma weight residual 1.520 1.572 -0.052 4.80e-03 4.34e+04 1.17e+02 bond pdb=" CZ3 TRP H 160 " pdb=" HZ3 TRP H 160 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N TYR L 41 " pdb=" H TYR L 41 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N THR L 169 " pdb=" H THR L 169 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" CH2 TRP H 109 " pdb=" HH2 TRP H 109 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 10806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 18295 4.69 - 9.39: 1086 9.39 - 14.08: 29 14.08 - 18.78: 3 18.78 - 23.47: 1 Bond angle restraints: 19414 Sorted by residual: angle pdb=" O GLN U 78 " pdb=" C GLN U 78 " pdb=" N GLY U 79 " ideal model delta sigma weight residual 120.83 97.36 23.47 7.40e-01 1.83e+00 1.01e+03 angle pdb=" CA GLU U 106 " pdb=" C GLU U 106 " pdb=" O GLU U 106 " ideal model delta sigma weight residual 120.42 109.39 11.03 1.06e+00 8.90e-01 1.08e+02 angle pdb=" CA GLU U 106 " pdb=" C GLU U 106 " pdb=" N ARG U 107 " ideal model delta sigma weight residual 117.39 128.07 -10.68 1.24e+00 6.50e-01 7.42e+01 angle pdb=" C TYR U 87 " pdb=" N SER U 88 " pdb=" CA SER U 88 " ideal model delta sigma weight residual 121.54 137.89 -16.35 1.91e+00 2.74e-01 7.33e+01 angle pdb=" C GLY U 60 " pdb=" N LEU U 61 " pdb=" CA LEU U 61 " ideal model delta sigma weight residual 121.54 136.13 -14.59 1.91e+00 2.74e-01 5.83e+01 ... (remaining 19409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 4754 20.80 - 41.59: 376 41.59 - 62.39: 143 62.39 - 83.18: 28 83.18 - 103.98: 7 Dihedral angle restraints: 5308 sinusoidal: 2958 harmonic: 2350 Sorted by residual: dihedral pdb=" CA VAL L 99 " pdb=" C VAL L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta harmonic sigma weight residual 180.00 146.53 33.47 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" C VAL H 217 " pdb=" N VAL H 217 " pdb=" CA VAL H 217 " pdb=" CB VAL H 217 " ideal model delta harmonic sigma weight residual -122.00 -137.61 15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" CA GLN U 78 " pdb=" C GLN U 78 " pdb=" N GLY U 79 " pdb=" CA GLY U 79 " ideal model delta harmonic sigma weight residual 180.00 149.06 30.94 0 5.00e+00 4.00e-02 3.83e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 657 0.128 - 0.257: 178 0.257 - 0.385: 29 0.385 - 0.514: 5 0.514 - 0.642: 2 Chirality restraints: 871 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.22e+01 chirality pdb=" CA PRO H 153 " pdb=" N PRO H 153 " pdb=" C PRO H 153 " pdb=" CB PRO H 153 " both_signs ideal model delta sigma weight residual False 2.72 2.08 0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 868 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN U 200 " -0.261 2.00e-02 2.50e+03 2.02e-01 6.13e+02 pdb=" CG ASN U 200 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN U 200 " 0.199 2.00e-02 2.50e+03 pdb=" ND2 ASN U 200 " 0.054 2.00e-02 2.50e+03 pdb="HD21 ASN U 200 " 0.234 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN U 172 " 0.268 2.00e-02 2.50e+03 2.01e-01 6.05e+02 pdb=" CG ASN U 172 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN U 172 " -0.164 2.00e-02 2.50e+03 pdb=" ND2 ASN U 172 " -0.046 2.00e-02 2.50e+03 pdb="HD21 ASN U 172 " -0.256 2.00e-02 2.50e+03 pdb=" C1 NAG U 301 " 0.266 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN U 78 " -0.111 2.00e-02 2.50e+03 1.99e-01 3.97e+02 pdb=" C GLN U 78 " 0.344 2.00e-02 2.50e+03 pdb=" O GLN U 78 " -0.136 2.00e-02 2.50e+03 pdb=" N GLY U 79 " -0.097 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 590 2.10 - 2.72: 15559 2.72 - 3.35: 30953 3.35 - 3.97: 40297 3.97 - 4.60: 59094 Nonbonded interactions: 146493 Sorted by model distance: nonbonded pdb=" HB3 GLN U 78 " pdb=" H GLY U 79 " model vdw 1.471 2.270 nonbonded pdb=" OD1 ASP U 102 " pdb=" HG SER U 104 " model vdw 1.551 2.450 nonbonded pdb=" O SER U 156 " pdb=" HG SER U 245 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR H 100 " pdb=" OD2 ASP H 108 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP U 22 " pdb=" HG SER U 48 " model vdw 1.581 2.450 ... (remaining 146488 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=0.33 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.070 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3636 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 : 0.015 0.078 5654 Z= 0.936 Angle : 2.333 23.472 7695 Z= 1.535 Chirality : 0.120 0.642 871 Planarity : 0.018 0.199 981 Dihedral : 17.151 103.980 2158 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 2.71 % Allowed : 11.55 % Favored : 85.73 % Rotamer: Outliers : 5.12 % Allowed : 8.32 % Favored : 86.56 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % Twisted General : 0.15 % 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: -2.94 (0.28), residues: 701 helix: -5.01 (0.21), residues: 12 sheet: -1.07 (0.39), residues: 164 loop : -2.36 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 137 TYR 0.157 0.027 TYR U 236 PHE 0.082 0.022 PHE H 172 TRP 0.167 0.030 TRP H 160 HIS 0.018 0.004 HIS U 249 Details of bonding type rmsd covalent geometry : bond 0.01459 ( 5630) covalent geometry : angle 2.32134 ( 7640) SS BOND : bond 0.01710 ( 17) SS BOND : angle 2.48712 ( 34) hydrogen bonds : bond 0.17739 ( 97) hydrogen bonds : angle 9.74763 ( 225) link_BETA1-4 : bond 0.03348 ( 3) link_BETA1-4 : angle 5.84258 ( 9) link_NAG-ASN : bond 0.01836 ( 4) link_NAG-ASN : angle 3.91522 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 65 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.4461 (t0) REVERT: L 159 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5426 (tm-30) REVERT: U 143 HIS cc_start: 0.7709 (t70) cc_final: 0.7404 (t70) REVERT: H 115 VAL cc_start: 0.3383 (OUTLIER) cc_final: 0.3141 (p) outliers start: 32 outliers final: 13 residues processed: 96 average time/residue: 0.1839 time to fit residues: 22.3416 Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN L 162 ASN U 128 HIS ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 233 ASN H 139 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.064106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.050469 restraints weight = 262048.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.051945 restraints weight = 200828.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.053282 restraints weight = 157759.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.054228 restraints weight = 130789.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.055044 restraints weight = 113494.490| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 5654 Z= 0.295 Angle : 1.093 10.209 7695 Z= 0.573 Chirality : 0.051 0.300 871 Planarity : 0.009 0.145 981 Dihedral : 12.340 82.845 907 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.84 % Favored : 87.59 % Rotamer: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % Twisted General : 0.89 % 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: -3.50 (0.28), residues: 701 helix: -3.99 (0.55), residues: 25 sheet: -1.58 (0.35), residues: 214 loop : -2.76 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 137 TYR 0.026 0.003 TYR U 236 PHE 0.022 0.003 PHE L 123 TRP 0.020 0.003 TRP H 160 HIS 0.014 0.003 HIS U 249 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 5630) covalent geometry : angle 1.06216 ( 7640) SS BOND : bond 0.00456 ( 17) SS BOND : angle 1.64026 ( 34) hydrogen bonds : bond 0.05890 ( 97) hydrogen bonds : angle 8.96603 ( 225) link_BETA1-4 : bond 0.01876 ( 3) link_BETA1-4 : angle 4.41083 ( 9) link_NAG-ASN : bond 0.01920 ( 4) link_NAG-ASN : angle 5.02729 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7695 (mtp) cc_final: 0.7269 (mtp) REVERT: U 57 TYR cc_start: 0.8995 (p90) cc_final: 0.8762 (p90) REVERT: U 94 GLU cc_start: 0.9186 (tt0) cc_final: 0.8802 (tp30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2290 time to fit residues: 14.2409 Evaluate side-chains 38 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.060838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.047502 restraints weight = 262496.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.049234 restraints weight = 184851.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 76)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.050775 restraints weight = 142823.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.051611 restraints weight = 118223.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.052288 restraints weight = 103754.083| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5654 Z= 0.215 Angle : 0.895 7.335 7695 Z= 0.468 Chirality : 0.048 0.292 871 Planarity : 0.008 0.133 981 Dihedral : 10.430 67.725 907 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.12 % Favored : 86.45 % Rotamer: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % Twisted General : 0.60 % 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: -3.95 (0.27), residues: 701 helix: -3.22 (0.82), residues: 25 sheet: -2.31 (0.31), residues: 239 loop : -2.89 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 66 TYR 0.020 0.002 TYR L 92 PHE 0.029 0.003 PHE L 67 TRP 0.014 0.003 TRP H 109 HIS 0.008 0.002 HIS U 249 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 5630) covalent geometry : angle 0.87659 ( 7640) SS BOND : bond 0.00522 ( 17) SS BOND : angle 1.52765 ( 34) hydrogen bonds : bond 0.04791 ( 97) hydrogen bonds : angle 8.80338 ( 225) link_BETA1-4 : bond 0.00983 ( 3) link_BETA1-4 : angle 3.01944 ( 9) link_NAG-ASN : bond 0.00996 ( 4) link_NAG-ASN : angle 3.37091 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 4 MET cc_start: 0.7717 (mtp) cc_final: 0.7416 (mtp) REVERT: U 143 HIS cc_start: 0.7595 (t70) cc_final: 0.7186 (t70) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.2569 time to fit residues: 12.6520 Evaluate side-chains 31 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.051892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.041189 restraints weight = 310285.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.041975 restraints weight = 256738.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.042545 restraints weight = 223945.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.043040 restraints weight = 200153.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.043276 restraints weight = 183062.781| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5654 Z= 0.156 Angle : 0.802 10.032 7695 Z= 0.418 Chirality : 0.046 0.279 871 Planarity : 0.007 0.136 981 Dihedral : 9.465 57.534 907 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.84 % Favored : 86.73 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.88 (0.28), residues: 701 helix: -3.09 (0.97), residues: 19 sheet: -2.43 (0.30), residues: 250 loop : -2.73 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 160 TYR 0.014 0.002 TYR U 92 PHE 0.021 0.002 PHE U 167 TRP 0.011 0.002 TRP H 160 HIS 0.016 0.002 HIS U 229 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5630) covalent geometry : angle 0.78175 ( 7640) SS BOND : bond 0.00572 ( 17) SS BOND : angle 1.72157 ( 34) hydrogen bonds : bond 0.04096 ( 97) hydrogen bonds : angle 8.54907 ( 225) link_BETA1-4 : bond 0.00852 ( 3) link_BETA1-4 : angle 3.22335 ( 9) link_NAG-ASN : bond 0.00938 ( 4) link_NAG-ASN : angle 2.71662 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 129 GLN cc_start: 0.9053 (tt0) cc_final: 0.8559 (tt0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2065 time to fit residues: 8.8360 Evaluate side-chains 29 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.051036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.040246 restraints weight = 301952.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.041017 restraints weight = 246499.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.041578 restraints weight = 215344.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.042057 restraints weight = 192815.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.042422 restraints weight = 176053.767| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5654 Z= 0.156 Angle : 0.754 9.200 7695 Z= 0.392 Chirality : 0.044 0.202 871 Planarity : 0.007 0.115 981 Dihedral : 8.780 50.129 907 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.55 % Favored : 87.02 % Rotamer: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.03 (0.28), residues: 701 helix: -3.22 (0.87), residues: 19 sheet: -2.57 (0.28), residues: 269 loop : -2.78 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 142 TYR 0.014 0.002 TYR U 92 PHE 0.012 0.002 PHE H 106 TRP 0.010 0.002 TRP H 47 HIS 0.019 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5630) covalent geometry : angle 0.73904 ( 7640) SS BOND : bond 0.00530 ( 17) SS BOND : angle 1.59397 ( 34) hydrogen bonds : bond 0.03884 ( 97) hydrogen bonds : angle 8.53590 ( 225) link_BETA1-4 : bond 0.00693 ( 3) link_BETA1-4 : angle 2.72201 ( 9) link_NAG-ASN : bond 0.00750 ( 4) link_NAG-ASN : angle 2.11256 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1886 time to fit residues: 9.0955 Evaluate side-chains 29 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.051803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.047055 restraints weight = 274175.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.047429 restraints weight = 244410.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.047735 restraints weight = 221016.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.047893 restraints weight = 202353.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.048167 restraints weight = 191397.140| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5654 Z= 0.137 Angle : 0.722 6.045 7695 Z= 0.380 Chirality : 0.044 0.263 871 Planarity : 0.007 0.118 981 Dihedral : 8.467 49.201 907 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.41 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.91 (0.28), residues: 701 helix: -2.96 (0.95), residues: 19 sheet: -2.47 (0.30), residues: 249 loop : -2.76 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 160 TYR 0.012 0.001 TYR U 92 PHE 0.024 0.002 PHE L 123 TRP 0.010 0.002 TRP H 47 HIS 0.010 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5630) covalent geometry : angle 0.70752 ( 7640) SS BOND : bond 0.00366 ( 17) SS BOND : angle 1.55783 ( 34) hydrogen bonds : bond 0.03772 ( 97) hydrogen bonds : angle 8.28176 ( 225) link_BETA1-4 : bond 0.00788 ( 3) link_BETA1-4 : angle 2.52852 ( 9) link_NAG-ASN : bond 0.00694 ( 4) link_NAG-ASN : angle 1.95931 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1926 time to fit residues: 9.0812 Evaluate side-chains 28 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.050522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.045614 restraints weight = 278228.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.046062 restraints weight = 243832.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.046387 restraints weight = 217330.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.046691 restraints weight = 197450.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.046931 restraints weight = 181149.142| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5654 Z= 0.145 Angle : 0.704 8.340 7695 Z= 0.368 Chirality : 0.043 0.214 871 Planarity : 0.007 0.098 981 Dihedral : 8.107 47.274 907 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.27 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % 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: -3.90 (0.28), residues: 701 helix: -2.81 (0.93), residues: 19 sheet: -2.48 (0.29), residues: 255 loop : -2.73 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 160 TYR 0.013 0.002 TYR H 128 PHE 0.018 0.002 PHE H 106 TRP 0.011 0.002 TRP L 168 HIS 0.010 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5630) covalent geometry : angle 0.69142 ( 7640) SS BOND : bond 0.00380 ( 17) SS BOND : angle 1.42001 ( 34) hydrogen bonds : bond 0.03673 ( 97) hydrogen bonds : angle 8.09931 ( 225) link_BETA1-4 : bond 0.00698 ( 3) link_BETA1-4 : angle 2.32137 ( 9) link_NAG-ASN : bond 0.00596 ( 4) link_NAG-ASN : angle 1.83537 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1949 time to fit residues: 8.4046 Evaluate side-chains 28 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.055154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.043160 restraints weight = 271009.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.044769 restraints weight = 191212.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.046104 restraints weight = 145070.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.046944 restraints weight = 118757.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.047576 restraints weight = 103342.835| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 5654 Z= 0.251 Angle : 0.854 7.712 7695 Z= 0.445 Chirality : 0.046 0.262 871 Planarity : 0.008 0.128 981 Dihedral : 8.763 59.249 907 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.69 % Favored : 84.74 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % 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: -4.17 (0.28), residues: 701 helix: -2.39 (0.98), residues: 19 sheet: -2.71 (0.31), residues: 229 loop : -2.96 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 160 TYR 0.028 0.003 TYR H 104 PHE 0.017 0.003 PHE H 152 TRP 0.034 0.004 TRP L 153 HIS 0.012 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 5630) covalent geometry : angle 0.83867 ( 7640) SS BOND : bond 0.00692 ( 17) SS BOND : angle 1.98485 ( 34) hydrogen bonds : bond 0.04355 ( 97) hydrogen bonds : angle 8.74042 ( 225) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 2.31723 ( 9) link_NAG-ASN : bond 0.00456 ( 4) link_NAG-ASN : angle 2.12590 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1665 time to fit residues: 6.1275 Evaluate side-chains 25 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.045978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.035823 restraints weight = 333856.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.036484 restraints weight = 280347.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.037006 restraints weight = 246758.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.037414 restraints weight = 222447.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.037717 restraints weight = 204616.944| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.7800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 5654 Z= 0.221 Angle : 0.809 8.173 7695 Z= 0.422 Chirality : 0.045 0.252 871 Planarity : 0.007 0.059 981 Dihedral : 8.766 53.061 907 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.27 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % 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: -4.34 (0.28), residues: 701 helix: -2.44 (0.95), residues: 19 sheet: -2.81 (0.31), residues: 240 loop : -3.08 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 82 TYR 0.013 0.002 TYR H 104 PHE 0.017 0.002 PHE L 67 TRP 0.019 0.003 TRP L 168 HIS 0.010 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 5630) covalent geometry : angle 0.79486 ( 7640) SS BOND : bond 0.00481 ( 17) SS BOND : angle 1.86505 ( 34) hydrogen bonds : bond 0.04159 ( 97) hydrogen bonds : angle 8.84697 ( 225) link_BETA1-4 : bond 0.00459 ( 3) link_BETA1-4 : angle 2.13302 ( 9) link_NAG-ASN : bond 0.00522 ( 4) link_NAG-ASN : angle 2.03328 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1666 time to fit residues: 5.8003 Evaluate side-chains 22 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.045390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.035151 restraints weight = 323032.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.035741 restraints weight = 274367.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.036186 restraints weight = 243307.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.036533 restraints weight = 223192.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.036790 restraints weight = 207773.708| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5654 Z= 0.178 Angle : 0.753 6.408 7695 Z= 0.393 Chirality : 0.043 0.243 871 Planarity : 0.007 0.053 981 Dihedral : 8.401 42.128 907 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.12 % Favored : 85.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % Twisted General : 0.15 % 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: -4.25 (0.28), residues: 701 helix: -2.52 (0.96), residues: 19 sheet: -2.76 (0.31), residues: 241 loop : -2.99 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 116 TYR 0.012 0.002 TYR U 236 PHE 0.015 0.002 PHE L 67 TRP 0.013 0.002 TRP L 168 HIS 0.010 0.002 HIS U 229 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5630) covalent geometry : angle 0.74107 ( 7640) SS BOND : bond 0.00417 ( 17) SS BOND : angle 1.57376 ( 34) hydrogen bonds : bond 0.03915 ( 97) hydrogen bonds : angle 8.60985 ( 225) link_BETA1-4 : bond 0.00546 ( 3) link_BETA1-4 : angle 2.03728 ( 9) link_NAG-ASN : bond 0.00494 ( 4) link_NAG-ASN : angle 2.01042 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1765 time to fit residues: 5.3992 Evaluate side-chains 22 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.050837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.039538 restraints weight = 306213.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.041071 restraints weight = 218996.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.042208 restraints weight = 169246.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.042594 restraints weight = 139399.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.043050 restraints weight = 123423.218| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.8292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5654 Z= 0.163 Angle : 0.728 6.350 7695 Z= 0.379 Chirality : 0.043 0.235 871 Planarity : 0.006 0.054 981 Dihedral : 8.001 41.127 907 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.98 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.30 % Twisted Proline : 2.94 % Twisted General : 0.15 % 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: -4.20 (0.28), residues: 701 helix: -2.76 (0.81), residues: 25 sheet: -2.71 (0.31), residues: 229 loop : -2.96 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 116 TYR 0.012 0.002 TYR U 92 PHE 0.013 0.002 PHE U 167 TRP 0.012 0.002 TRP H 47 HIS 0.009 0.002 HIS U 160 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5630) covalent geometry : angle 0.71634 ( 7640) SS BOND : bond 0.00380 ( 17) SS BOND : angle 1.49954 ( 34) hydrogen bonds : bond 0.03709 ( 97) hydrogen bonds : angle 8.50068 ( 225) link_BETA1-4 : bond 0.00614 ( 3) link_BETA1-4 : angle 2.00412 ( 9) link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 2.05662 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.47 seconds wall clock time: 46 minutes 57.63 seconds (2817.63 seconds total)