Starting phenix.real_space_refine on Thu Jul 2 01:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qbc_13886/07_2026/7qbc_13886.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3400 2.51 5 N 728 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5054 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.17, per 1000 atoms: 0.23 Number of scatterers: 5054 At special positions: 0 Unit cell: (75.9, 78.1, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 904 8.00 N 728 7.00 C 3400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 169.6 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 73.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 37 through 73 removed outlier: 3.520A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.865A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.514A pdb=" N GLY A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.731A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 removed outlier: 3.642A pdb=" N THR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 37 through 73 removed outlier: 3.519A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.864A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.513A pdb=" N GLY B 163 " --> pdb=" O PHE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 237 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 249' Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.732A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 297 removed outlier: 3.641A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR A 26 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 33 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR B 26 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 33 " --> pdb=" O TYR B 26 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 738 1.31 - 1.44: 1336 1.44 - 1.56: 3062 1.56 - 1.69: 14 1.69 - 1.81: 40 Bond restraints: 5190 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 5185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6615 1.64 - 3.27: 418 3.27 - 4.91: 98 4.91 - 6.54: 30 6.54 - 8.18: 5 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" C TYR A 181 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" N TYR B 181 " pdb=" CA TYR B 181 " pdb=" C TYR B 181 " ideal model delta sigma weight residual 111.28 105.94 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" N MET B 294 " pdb=" CA MET B 294 " pdb=" C MET B 294 " ideal model delta sigma weight residual 113.28 107.62 5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N MET A 294 " pdb=" CA MET A 294 " pdb=" C MET A 294 " ideal model delta sigma weight residual 113.28 107.67 5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N MET B 69 " pdb=" CA MET B 69 " pdb=" C MET B 69 " ideal model delta sigma weight residual 111.28 106.32 4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 2548 15.42 - 30.84: 239 30.84 - 46.25: 59 46.25 - 61.67: 20 61.67 - 77.09: 8 Dihedral angle restraints: 2874 sinusoidal: 1048 harmonic: 1826 Sorted by residual: dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N GLY B 56 " pdb=" CA GLY B 56 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N GLY A 56 " pdb=" CA GLY A 56 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR B 144 " pdb=" C THR B 144 " pdb=" N SER B 145 " pdb=" CA SER B 145 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 650 0.046 - 0.092: 202 0.092 - 0.138: 50 0.138 - 0.184: 12 0.184 - 0.230: 2 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB VAL B 191 " pdb=" CA VAL B 191 " pdb=" CG1 VAL B 191 " pdb=" CG2 VAL B 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL A 191 " pdb=" CA VAL A 191 " pdb=" CG1 VAL A 191 " pdb=" CG2 VAL A 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 913 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 293 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 293 " -0.075 2.00e-02 2.50e+03 pdb=" O SER A 293 " 0.029 2.00e-02 2.50e+03 pdb=" N MET A 294 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 293 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C SER B 293 " 0.074 2.00e-02 2.50e+03 pdb=" O SER B 293 " -0.028 2.00e-02 2.50e+03 pdb=" N MET B 294 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 179 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A 179 " 0.071 2.00e-02 2.50e+03 pdb=" O THR A 179 " -0.027 2.00e-02 2.50e+03 pdb=" N MET A 180 " -0.024 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 40 2.62 - 3.19: 4851 3.19 - 3.76: 7546 3.76 - 4.33: 10065 4.33 - 4.90: 16455 Nonbonded interactions: 38957 Sorted by model distance: nonbonded pdb=" O LYS B 100 " pdb=" OG SER B 104 " model vdw 2.055 3.040 nonbonded pdb=" O LYS A 100 " pdb=" OG SER A 104 " model vdw 2.056 3.040 nonbonded pdb=" O LEU B 102 " pdb=" OG SER B 107 " model vdw 2.194 3.040 nonbonded pdb=" O LEU A 102 " pdb=" OG SER A 107 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A 142 " pdb=" OG SER A 145 " model vdw 2.210 3.040 ... (remaining 38952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.310 Find NCS groups from input model: 0.020 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.008 0.108 5194 Z= 0.394 Angle : 0.975 8.181 7178 Z= 0.532 Chirality : 0.049 0.230 916 Planarity : 0.007 0.047 812 Dihedral : 14.349 77.087 1694 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.31), residues: 614 helix: -1.04 (0.24), residues: 414 sheet: -3.35 (1.02), residues: 24 loop : -2.33 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.025 0.002 TYR B 193 PHE 0.034 0.002 PHE A 262 TRP 0.026 0.004 TRP A 70 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.39 ( 5190) covalent geometry : angle 0.97480 / 0.53 ( 7166) hydrogen bonds : bond 0.14335 / 8.86 ( 332) hydrogen bonds : angle 6.98824 / 4.92 ( 966) link_NAG-ASN : bond 0.00059 / 0.03 ( 4) link_NAG-ASN : angle 0.98719 / 0.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.172 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.0394 time to fit residues: 6.0304 Evaluate side-chains 87 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN A 253 GLN B 205 ASN B 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163556 restraints weight = 6601.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167311 restraints weight = 3830.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169967 restraints weight = 2810.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.171201 restraints weight = 2326.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172439 restraints weight = 2094.995| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5194 Z= 0.155 Angle : 0.637 6.713 7178 Z= 0.314 Chirality : 0.042 0.139 916 Planarity : 0.005 0.061 812 Dihedral : 9.251 59.842 812 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.06 % Allowed : 10.21 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.34), residues: 614 helix: 0.73 (0.26), residues: 408 sheet: -3.06 (1.18), residues: 20 loop : -1.86 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.014 0.001 TYR B 17 PHE 0.029 0.002 PHE B 244 TRP 0.015 0.002 TRP B 295 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5190) covalent geometry : angle 0.63515 / 0.31 ( 7166) hydrogen bonds : bond 0.04149 / 2.77 ( 332) hydrogen bonds : angle 4.48054 / 3.10 ( 966) link_NAG-ASN : bond 0.00281 / 0.13 ( 4) link_NAG-ASN : angle 1.24376 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.148 Fit side-chains REVERT: A 69 MET cc_start: 0.7582 (mmm) cc_final: 0.7297 (mmm) REVERT: A 111 TYR cc_start: 0.8597 (t80) cc_final: 0.8204 (t80) REVERT: B 69 MET cc_start: 0.7601 (mmm) cc_final: 0.7325 (mmm) REVERT: B 205 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7238 (t0) outliers start: 5 outliers final: 2 residues processed: 111 average time/residue: 0.0438 time to fit residues: 6.5758 Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 205 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN I 2 HIS K 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.192005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.161401 restraints weight = 6631.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165173 restraints weight = 3944.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167708 restraints weight = 2948.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169396 restraints weight = 2454.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169396 restraints weight = 2184.486| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5194 Z= 0.126 Angle : 0.591 5.916 7178 Z= 0.295 Chirality : 0.040 0.126 916 Planarity : 0.005 0.074 812 Dihedral : 9.111 59.879 812 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.91 % Allowed : 10.85 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.34), residues: 614 helix: 1.33 (0.26), residues: 412 sheet: -2.83 (1.22), residues: 20 loop : -1.77 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 76 TYR 0.010 0.001 TYR A 17 PHE 0.015 0.001 PHE B 55 TRP 0.017 0.002 TRP B 295 HIS 0.002 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 5190) covalent geometry : angle 0.58847 / 0.29 ( 7166) hydrogen bonds : bond 0.03610 / 2.42 ( 332) hydrogen bonds : angle 3.96785 / 2.74 ( 966) link_NAG-ASN : bond 0.00200 / 0.09 ( 4) link_NAG-ASN : angle 1.36706 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.177 Fit side-chains REVERT: A 69 MET cc_start: 0.7516 (mmm) cc_final: 0.7241 (mmm) REVERT: B 69 MET cc_start: 0.7554 (mmm) cc_final: 0.7267 (mmm) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.0605 time to fit residues: 8.7215 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 205 ASN B 85 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145145 restraints weight = 6669.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148942 restraints weight = 3836.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151398 restraints weight = 2817.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152658 restraints weight = 2355.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153038 restraints weight = 2137.154| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5194 Z= 0.203 Angle : 0.669 7.552 7178 Z= 0.326 Chirality : 0.043 0.135 916 Planarity : 0.005 0.074 812 Dihedral : 10.094 59.136 812 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.62 % Allowed : 13.40 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.34), residues: 614 helix: 1.48 (0.26), residues: 416 sheet: -2.81 (1.14), residues: 20 loop : -1.66 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.014 0.002 TYR B 98 PHE 0.027 0.002 PHE A 244 TRP 0.019 0.002 TRP B 295 HIS 0.003 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 ( 5190) covalent geometry : angle 0.66648 / 0.33 ( 7166) hydrogen bonds : bond 0.03920 / 2.64 ( 332) hydrogen bonds : angle 3.92933 / 2.73 ( 966) link_NAG-ASN : bond 0.00030 / 0.01 ( 4) link_NAG-ASN : angle 1.59814 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.141 Fit side-chains REVERT: A 295 TRP cc_start: 0.7790 (t-100) cc_final: 0.7500 (t-100) REVERT: B 76 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6851 (mtt-85) REVERT: B 205 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7489 (t0) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.0466 time to fit residues: 7.3237 Evaluate side-chains 100 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148597 restraints weight = 6784.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152308 restraints weight = 4008.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154672 restraints weight = 2985.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155615 restraints weight = 2520.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156364 restraints weight = 2324.085| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5194 Z= 0.127 Angle : 0.589 7.045 7178 Z= 0.291 Chirality : 0.039 0.122 916 Planarity : 0.005 0.074 812 Dihedral : 10.047 59.282 812 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.34 % Allowed : 18.51 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.35), residues: 614 helix: 1.71 (0.26), residues: 414 sheet: -3.04 (1.07), residues: 20 loop : -1.53 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.012 0.001 TYR B 98 PHE 0.016 0.001 PHE B 55 TRP 0.009 0.001 TRP A 70 HIS 0.002 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5190) covalent geometry : angle 0.58695 / 0.29 ( 7166) hydrogen bonds : bond 0.03375 / 2.26 ( 332) hydrogen bonds : angle 3.74108 / 2.60 ( 966) link_NAG-ASN : bond 0.00127 / 0.05 ( 4) link_NAG-ASN : angle 1.41672 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.110 Fit side-chains REVERT: A 76 ARG cc_start: 0.6837 (mtm-85) cc_final: 0.6627 (mtm-85) REVERT: A 295 TRP cc_start: 0.7772 (t-100) cc_final: 0.7543 (t-100) REVERT: B 295 TRP cc_start: 0.7762 (t-100) cc_final: 0.7377 (t-100) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 0.0532 time to fit residues: 8.0011 Evaluate side-chains 105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.178241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146964 restraints weight = 6771.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150419 restraints weight = 4064.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152663 restraints weight = 3059.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153873 restraints weight = 2585.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154131 restraints weight = 2353.376| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5194 Z= 0.149 Angle : 0.596 7.346 7178 Z= 0.294 Chirality : 0.040 0.126 916 Planarity : 0.005 0.074 812 Dihedral : 10.311 67.937 812 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.13 % Allowed : 20.85 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.35), residues: 614 helix: 1.85 (0.25), residues: 414 sheet: -2.87 (1.10), residues: 20 loop : -1.32 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 76 TYR 0.013 0.001 TYR B 98 PHE 0.016 0.001 PHE B 55 TRP 0.009 0.001 TRP B 70 HIS 0.002 0.001 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 5190) covalent geometry : angle 0.59367 / 0.29 ( 7166) hydrogen bonds : bond 0.03295 / 2.22 ( 332) hydrogen bonds : angle 3.72559 / 2.58 ( 966) link_NAG-ASN : bond 0.00079 / 0.03 ( 4) link_NAG-ASN : angle 1.45271 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.120 Fit side-chains REVERT: A 76 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6653 (mtt-85) REVERT: A 104 SER cc_start: 0.8873 (m) cc_final: 0.8597 (p) REVERT: A 205 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7331 (m-40) REVERT: B 85 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7662 (tt0) REVERT: B 295 TRP cc_start: 0.7844 (t-100) cc_final: 0.7543 (t-100) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.0497 time to fit residues: 6.9929 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 205 ASN B 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.177258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144993 restraints weight = 6697.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148780 restraints weight = 3876.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150881 restraints weight = 2869.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152558 restraints weight = 2432.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153192 restraints weight = 2187.368| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5194 Z= 0.143 Angle : 0.595 6.862 7178 Z= 0.294 Chirality : 0.040 0.125 916 Planarity : 0.005 0.073 812 Dihedral : 10.258 75.801 812 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.77 % Allowed : 20.85 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.35), residues: 614 helix: 1.91 (0.25), residues: 414 sheet: -2.93 (1.07), residues: 20 loop : -1.23 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.012 0.001 TYR B 98 PHE 0.014 0.001 PHE B 55 TRP 0.024 0.002 TRP A 295 HIS 0.002 0.001 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 5190) covalent geometry : angle 0.59228 / 0.29 ( 7166) hydrogen bonds : bond 0.03242 / 2.18 ( 332) hydrogen bonds : angle 3.70220 / 2.57 ( 966) link_NAG-ASN : bond 0.00080 / 0.04 ( 4) link_NAG-ASN : angle 1.40983 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.126 Fit side-chains REVERT: B 85 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7612 (tt0) REVERT: B 113 LEU cc_start: 0.8694 (mp) cc_final: 0.8481 (mt) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.0479 time to fit residues: 6.8047 Evaluate side-chains 101 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 205 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145649 restraints weight = 6699.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149493 restraints weight = 3871.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151808 restraints weight = 2851.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153270 restraints weight = 2396.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153946 restraints weight = 2165.938| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5194 Z= 0.146 Angle : 0.597 6.824 7178 Z= 0.296 Chirality : 0.040 0.127 916 Planarity : 0.005 0.073 812 Dihedral : 10.155 78.349 812 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.34 % Allowed : 21.91 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.35), residues: 614 helix: 1.93 (0.25), residues: 414 sheet: -2.86 (1.08), residues: 20 loop : -1.15 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.014 0.001 TYR B 106 PHE 0.015 0.001 PHE B 55 TRP 0.031 0.002 TRP B 295 HIS 0.002 0.000 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 5190) covalent geometry : angle 0.59484 / 0.30 ( 7166) hydrogen bonds : bond 0.03222 / 2.17 ( 332) hydrogen bonds : angle 3.72034 / 2.57 ( 966) link_NAG-ASN : bond 0.00056 / 0.02 ( 4) link_NAG-ASN : angle 1.42673 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.105 Fit side-chains REVERT: B 85 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7629 (tt0) REVERT: B 113 LEU cc_start: 0.8701 (mp) cc_final: 0.8485 (mt) REVERT: B 165 MET cc_start: 0.7236 (ttt) cc_final: 0.6934 (ttp) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.0416 time to fit residues: 6.6789 Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143007 restraints weight = 6716.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146752 restraints weight = 3980.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149058 restraints weight = 2993.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150252 restraints weight = 2538.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150669 restraints weight = 2320.172| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5194 Z= 0.160 Angle : 0.620 7.041 7178 Z= 0.306 Chirality : 0.041 0.136 916 Planarity : 0.005 0.072 812 Dihedral : 10.136 80.511 812 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 22.55 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.35), residues: 614 helix: 1.92 (0.25), residues: 416 sheet: -2.86 (1.07), residues: 20 loop : -1.22 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.018 0.002 TYR B 106 PHE 0.019 0.001 PHE A 262 TRP 0.024 0.002 TRP B 295 HIS 0.002 0.001 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 5190) covalent geometry : angle 0.61762 / 0.31 ( 7166) hydrogen bonds : bond 0.03255 / 2.19 ( 332) hydrogen bonds : angle 3.72094 / 2.58 ( 966) link_NAG-ASN : bond 0.00047 / 0.02 ( 4) link_NAG-ASN : angle 1.42281 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.145 Fit side-chains REVERT: B 85 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7659 (tt0) REVERT: B 113 LEU cc_start: 0.8658 (mp) cc_final: 0.8428 (mt) REVERT: B 165 MET cc_start: 0.7331 (ttt) cc_final: 0.7032 (ttp) outliers start: 11 outliers final: 8 residues processed: 118 average time/residue: 0.0486 time to fit residues: 7.7748 Evaluate side-chains 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145893 restraints weight = 6651.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149692 restraints weight = 3865.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152051 restraints weight = 2858.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153333 restraints weight = 2400.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154412 restraints weight = 2177.306| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5194 Z= 0.142 Angle : 0.615 6.781 7178 Z= 0.309 Chirality : 0.041 0.139 916 Planarity : 0.005 0.073 812 Dihedral : 10.091 81.208 812 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.91 % Allowed : 22.77 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.35), residues: 614 helix: 1.91 (0.25), residues: 416 sheet: -2.89 (1.06), residues: 20 loop : -1.17 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.020 0.002 TYR B 17 PHE 0.017 0.001 PHE A 262 TRP 0.034 0.002 TRP B 295 HIS 0.001 0.000 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 5190) covalent geometry : angle 0.61243 / 0.31 ( 7166) hydrogen bonds : bond 0.03216 / 2.17 ( 332) hydrogen bonds : angle 3.69551 / 2.57 ( 966) link_NAG-ASN : bond 0.00066 / 0.03 ( 4) link_NAG-ASN : angle 1.39564 / 0.89 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.119 Fit side-chains REVERT: A 104 SER cc_start: 0.8970 (m) cc_final: 0.8719 (p) REVERT: A 205 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7491 (t0) REVERT: B 85 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7636 (tt0) REVERT: B 113 LEU cc_start: 0.8695 (mp) cc_final: 0.8466 (mt) REVERT: B 165 MET cc_start: 0.7266 (ttt) cc_final: 0.6968 (ttp) outliers start: 9 outliers final: 7 residues processed: 111 average time/residue: 0.0472 time to fit residues: 7.1430 Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 ASN ** 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 = 0.4114 r_free = 0.4114 target = 0.182123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151690 restraints weight = 6709.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155033 restraints weight = 4206.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156874 restraints weight = 3230.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158450 restraints weight = 2792.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158832 restraints weight = 2531.799| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5194 Z= 0.161 Angle : 1.077 59.198 7178 Z= 0.613 Chirality : 0.041 0.204 916 Planarity : 0.005 0.072 812 Dihedral : 10.098 81.226 812 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.49 % Allowed : 23.62 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.35), residues: 614 helix: 1.86 (0.25), residues: 416 sheet: -2.88 (1.06), residues: 20 loop : -1.18 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.016 0.002 TYR B 106 PHE 0.016 0.001 PHE A 262 TRP 0.029 0.002 TRP B 295 HIS 0.001 0.000 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 5190) covalent geometry : angle 1.07670 / 0.61 ( 7166) hydrogen bonds : bond 0.03370 / 2.32 ( 332) hydrogen bonds : angle 3.70354 / 2.58 ( 966) link_NAG-ASN : bond 0.00071 / 0.03 ( 4) link_NAG-ASN : angle 1.39357 / 0.89 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 718.82 seconds wall clock time: 13 minutes 6.58 seconds (786.58 seconds total)