Starting phenix.real_space_refine on Tue Mar 3 13:35:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qbc_13886/03_2026/7qbc_13886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qbc_13886/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qbc_13886/03_2026/7qbc_13886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qbc_13886/03_2026/7qbc_13886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qbc_13886/03_2026/7qbc_13886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qbc_13886/03_2026/7qbc_13886.map" } 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): 0.01s 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: 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.30, per 1000 atoms: 0.26 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: 0.45 Conformation dependent library (CDL) restraints added in 373.3 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: 0.13 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: 0.76 Time building geometry restraints manager: 0.58 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: 3284 15.42 - 30.84: 245 30.84 - 46.25: 83 46.25 - 61.67: 34 61.67 - 77.09: 8 Dihedral angle restraints: 3654 sinusoidal: 1828 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 3651 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: 1.260 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 : 13.182 77.087 2474 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 covalent geometry : bond 0.00790 ( 5190) covalent geometry : angle 0.97480 ( 7166) hydrogen bonds : bond 0.14335 ( 332) hydrogen bonds : angle 6.98824 ( 966) link_NAG-ASN : bond 0.00059 ( 4) link_NAG-ASN : angle 0.98719 ( 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 : 0.162 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.0514 time to fit residues: 7.7316 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 : 0.171 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4266 r_free = 0.4266 target = 0.197695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169461 restraints weight = 6568.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173109 restraints weight = 3892.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175157 restraints weight = 2875.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.176921 restraints weight = 2415.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.177353 restraints weight = 2147.010| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1788 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= 0.155 Angle : 0.647 6.981 7178 Z= 0.318 Chirality : 0.041 0.129 916 Planarity : 0.005 0.060 812 Dihedral : 9.348 59.127 1592 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.28 % Allowed : 9.79 % Favored : 88.94 % 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: -0.28 (0.33), residues: 614 helix: 0.74 (0.26), residues: 408 sheet: -3.07 (1.18), residues: 20 loop : -1.87 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.014 0.001 TYR B 17 PHE 0.028 0.002 PHE B 244 TRP 0.015 0.002 TRP B 295 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5190) covalent geometry : angle 0.64485 ( 7166) hydrogen bonds : bond 0.04095 ( 332) hydrogen bonds : angle 4.44866 ( 966) link_NAG-ASN : bond 0.00150 ( 4) link_NAG-ASN : angle 1.53151 ( 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 119 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.161 Fit side-chains REVERT: A 69 MET cc_start: 0.7605 (mmm) cc_final: 0.7310 (mmm) REVERT: A 111 TYR cc_start: 0.8622 (t80) cc_final: 0.8218 (t80) REVERT: B 69 MET cc_start: 0.7651 (mmm) cc_final: 0.7333 (mmm) REVERT: B 205 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7239 (t0) outliers start: 6 outliers final: 2 residues processed: 113 average time/residue: 0.0561 time to fit residues: 8.5096 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 205 ASN I 2 HIS B 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.191878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160734 restraints weight = 6617.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164658 restraints weight = 3825.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166869 restraints weight = 2820.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168476 restraints weight = 2376.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169541 restraints weight = 2126.509| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5194 Z= 0.130 Angle : 0.594 5.917 7178 Z= 0.296 Chirality : 0.040 0.125 916 Planarity : 0.005 0.072 812 Dihedral : 9.161 58.538 1592 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.49 % Allowed : 12.34 % Favored : 86.17 % 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: 0.39 (0.34), residues: 614 helix: 1.30 (0.26), residues: 412 sheet: -2.83 (1.21), residues: 20 loop : -1.78 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.010 0.001 TYR B 98 PHE 0.016 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 covalent geometry : bond 0.00292 ( 5190) covalent geometry : angle 0.59106 ( 7166) hydrogen bonds : bond 0.03643 ( 332) hydrogen bonds : angle 3.97810 ( 966) link_NAG-ASN : bond 0.00169 ( 4) link_NAG-ASN : angle 1.54234 ( 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 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.197 Fit side-chains REVERT: A 69 MET cc_start: 0.7560 (mmm) cc_final: 0.7269 (mmm) outliers start: 7 outliers final: 4 residues processed: 109 average time/residue: 0.0582 time to fit residues: 8.4003 Evaluate side-chains 100 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN 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: 1.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 205 ASN A 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.187296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155869 restraints weight = 6598.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159664 restraints weight = 3863.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162131 restraints weight = 2876.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163419 restraints weight = 2414.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164308 restraints weight = 2189.204| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5194 Z= 0.140 Angle : 0.601 7.123 7178 Z= 0.293 Chirality : 0.040 0.122 916 Planarity : 0.005 0.074 812 Dihedral : 9.099 56.814 1592 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.55 % Allowed : 14.47 % 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: 0.78 (0.35), residues: 614 helix: 1.61 (0.26), residues: 412 sheet: -2.79 (1.16), residues: 20 loop : -1.68 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.011 0.001 TYR B 98 PHE 0.015 0.001 PHE B 55 TRP 0.017 0.002 TRP B 295 HIS 0.001 0.000 HIS K 2 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5190) covalent geometry : angle 0.59761 ( 7166) hydrogen bonds : bond 0.03457 ( 332) hydrogen bonds : angle 3.79290 ( 966) link_NAG-ASN : bond 0.00126 ( 4) link_NAG-ASN : angle 1.56850 ( 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 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.153 Fit side-chains REVERT: A 295 TRP cc_start: 0.7794 (t-100) cc_final: 0.7368 (t-100) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.0560 time to fit residues: 8.4137 Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 253 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148967 restraints weight = 6819.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152913 restraints weight = 3914.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155519 restraints weight = 2875.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157012 restraints weight = 2393.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157673 restraints weight = 2158.292| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5194 Z= 0.137 Angle : 0.604 6.966 7178 Z= 0.296 Chirality : 0.040 0.124 916 Planarity : 0.005 0.072 812 Dihedral : 9.179 59.798 1592 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.70 % Allowed : 18.94 % Favored : 79.36 % 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: 0.91 (0.35), residues: 614 helix: 1.70 (0.26), residues: 412 sheet: -2.92 (1.11), residues: 20 loop : -1.58 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.011 0.001 TYR B 98 PHE 0.017 0.001 PHE B 262 TRP 0.009 0.001 TRP K 3 HIS 0.002 0.000 HIS K 2 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5190) covalent geometry : angle 0.60113 ( 7166) hydrogen bonds : bond 0.03376 ( 332) hydrogen bonds : angle 3.72102 ( 966) link_NAG-ASN : bond 0.00122 ( 4) link_NAG-ASN : angle 1.53576 ( 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 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.124 Fit side-chains REVERT: A 205 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7397 (m-40) REVERT: A 295 TRP cc_start: 0.7775 (t-100) cc_final: 0.7471 (t-100) REVERT: B 85 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7461 (tt0) REVERT: B 295 TRP cc_start: 0.7833 (t-100) cc_final: 0.7420 (t-100) outliers start: 8 outliers final: 4 residues processed: 109 average time/residue: 0.0578 time to fit residues: 8.4168 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4094 r_free = 0.4094 target = 0.180866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149209 restraints weight = 6754.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153211 restraints weight = 3759.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155473 restraints weight = 2714.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157192 restraints weight = 2270.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158014 restraints weight = 2024.145| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5194 Z= 0.155 Angle : 0.622 6.955 7178 Z= 0.305 Chirality : 0.040 0.121 916 Planarity : 0.005 0.072 812 Dihedral : 9.525 67.417 1592 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.49 % Allowed : 20.43 % Favored : 78.09 % 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: 1.05 (0.35), residues: 614 helix: 1.78 (0.26), residues: 414 sheet: -2.89 (1.11), residues: 20 loop : -1.47 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 76 TYR 0.011 0.001 TYR B 98 PHE 0.015 0.002 PHE B 55 TRP 0.008 0.001 TRP A 70 HIS 0.003 0.001 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5190) covalent geometry : angle 0.61912 ( 7166) hydrogen bonds : bond 0.03394 ( 332) hydrogen bonds : angle 3.71596 ( 966) link_NAG-ASN : bond 0.00088 ( 4) link_NAG-ASN : angle 1.53744 ( 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 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.151 Fit side-chains REVERT: A 69 MET cc_start: 0.7630 (mmm) cc_final: 0.7220 (tpp) REVERT: A 85 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7512 (tt0) REVERT: A 295 TRP cc_start: 0.7794 (t-100) cc_final: 0.7546 (t-100) REVERT: B 85 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7539 (tt0) REVERT: B 295 TRP cc_start: 0.7847 (t-100) cc_final: 0.7527 (t-100) outliers start: 7 outliers final: 6 residues processed: 110 average time/residue: 0.0627 time to fit residues: 9.1352 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 : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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 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: 0.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4092 r_free = 0.4092 target = 0.180843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149388 restraints weight = 6663.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153318 restraints weight = 3745.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155826 restraints weight = 2713.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157138 restraints weight = 2243.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157927 restraints weight = 2027.589| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5194 Z= 0.139 Angle : 0.611 7.008 7178 Z= 0.301 Chirality : 0.040 0.122 916 Planarity : 0.005 0.072 812 Dihedral : 9.650 75.172 1592 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.13 % Allowed : 21.06 % Favored : 76.81 % 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: 1.21 (0.35), residues: 614 helix: 1.88 (0.25), residues: 414 sheet: -2.87 (1.11), residues: 20 loop : -1.36 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 76 TYR 0.012 0.001 TYR B 98 PHE 0.015 0.001 PHE A 55 TRP 0.007 0.001 TRP A 70 HIS 0.001 0.000 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5190) covalent geometry : angle 0.60816 ( 7166) hydrogen bonds : bond 0.03266 ( 332) hydrogen bonds : angle 3.69571 ( 966) link_NAG-ASN : bond 0.00102 ( 4) link_NAG-ASN : angle 1.52530 ( 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 117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.171 Fit side-chains REVERT: A 69 MET cc_start: 0.7672 (mmm) cc_final: 0.7253 (tpp) REVERT: A 85 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7496 (tt0) REVERT: A 205 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 85 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7269 (mm-40) REVERT: B 295 TRP cc_start: 0.7829 (t-100) cc_final: 0.7531 (t-100) outliers start: 10 outliers final: 7 residues processed: 114 average time/residue: 0.0587 time to fit residues: 8.9906 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 : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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 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: 1.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 32 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.180575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149364 restraints weight = 6693.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152906 restraints weight = 4032.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155152 restraints weight = 3022.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156600 restraints weight = 2556.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157203 restraints weight = 2308.608| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5194 Z= 0.141 Angle : 0.619 6.970 7178 Z= 0.305 Chirality : 0.040 0.125 916 Planarity : 0.005 0.072 812 Dihedral : 9.568 78.946 1592 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 1.28 (0.35), residues: 614 helix: 1.91 (0.25), residues: 414 sheet: -2.82 (1.10), residues: 20 loop : -1.24 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 76 TYR 0.013 0.001 TYR B 98 PHE 0.017 0.001 PHE B 55 TRP 0.027 0.002 TRP A 295 HIS 0.002 0.000 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5190) covalent geometry : angle 0.61611 ( 7166) hydrogen bonds : bond 0.03234 ( 332) hydrogen bonds : angle 3.69569 ( 966) link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 1.50698 ( 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 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.160 Fit side-chains REVERT: A 69 MET cc_start: 0.7573 (mmm) cc_final: 0.7270 (tpp) REVERT: A 85 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7582 (tt0) REVERT: B 85 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7343 (mm-40) REVERT: B 165 MET cc_start: 0.7250 (ttt) cc_final: 0.6962 (ttp) outliers start: 9 outliers final: 7 residues processed: 112 average time/residue: 0.0592 time to fit residues: 8.7787 Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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: 2.9990 chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4075 r_free = 0.4075 target = 0.179177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148299 restraints weight = 6624.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151852 restraints weight = 3997.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154100 restraints weight = 3006.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155518 restraints weight = 2535.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156234 restraints weight = 2286.682| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5194 Z= 0.154 Angle : 0.615 7.284 7178 Z= 0.306 Chirality : 0.040 0.126 916 Planarity : 0.005 0.074 812 Dihedral : 9.470 81.977 1592 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.13 % Allowed : 21.91 % Favored : 75.96 % 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: -2.81 (1.10), residues: 20 loop : -1.16 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.013 0.001 TYR B 98 PHE 0.017 0.001 PHE B 55 TRP 0.032 0.003 TRP B 295 HIS 0.002 0.000 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5190) covalent geometry : angle 0.61201 ( 7166) hydrogen bonds : bond 0.03291 ( 332) hydrogen bonds : angle 3.70480 ( 966) link_NAG-ASN : bond 0.00064 ( 4) link_NAG-ASN : angle 1.54925 ( 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 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.221 Fit side-chains REVERT: A 69 MET cc_start: 0.7654 (mmm) cc_final: 0.7359 (tpp) REVERT: A 85 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7332 (mm-40) REVERT: A 269 LYS cc_start: 0.7131 (tptp) cc_final: 0.6906 (tptm) REVERT: B 85 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7376 (mm-40) REVERT: B 165 MET cc_start: 0.7207 (ttt) cc_final: 0.6926 (ttp) REVERT: B 269 LYS cc_start: 0.7210 (tptp) cc_final: 0.6933 (tptm) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.0599 time to fit residues: 8.8707 Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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: 0.6980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4074 r_free = 0.4074 target = 0.178838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147528 restraints weight = 6680.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151041 restraints weight = 4057.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152962 restraints weight = 3070.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154595 restraints weight = 2633.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155187 restraints weight = 2376.855| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5194 Z= 0.149 Angle : 0.611 7.481 7178 Z= 0.305 Chirality : 0.041 0.139 916 Planarity : 0.005 0.071 812 Dihedral : 9.378 83.204 1592 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.70 % Allowed : 22.55 % 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: 1.28 (0.35), residues: 614 helix: 1.89 (0.25), residues: 416 sheet: -2.79 (1.08), residues: 20 loop : -1.24 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.013 0.001 TYR B 98 PHE 0.017 0.001 PHE B 55 TRP 0.028 0.002 TRP B 295 HIS 0.002 0.000 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5190) covalent geometry : angle 0.60860 ( 7166) hydrogen bonds : bond 0.03265 ( 332) hydrogen bonds : angle 3.71030 ( 966) link_NAG-ASN : bond 0.00059 ( 4) link_NAG-ASN : angle 1.54336 ( 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: 8 poor density : 106 time to evaluate : 0.155 Fit side-chains REVERT: A 69 MET cc_start: 0.7655 (mmm) cc_final: 0.7358 (tpp) REVERT: A 85 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7358 (mm-40) REVERT: B 85 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7389 (mm-40) REVERT: B 165 MET cc_start: 0.7271 (ttt) cc_final: 0.6989 (ttp) outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.0580 time to fit residues: 8.6792 Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU 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: 0.8980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4075 r_free = 0.4075 target = 0.179147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147912 restraints weight = 6733.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151439 restraints weight = 4065.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.153695 restraints weight = 3065.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155041 restraints weight = 2596.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155679 restraints weight = 2353.956| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5194 Z= 0.196 Angle : 1.149 59.193 7178 Z= 0.699 Chirality : 0.040 0.126 916 Planarity : 0.005 0.072 812 Dihedral : 9.385 83.201 1592 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.49 % Allowed : 23.19 % Favored : 75.32 % Cbeta Deviations : 0.17 % 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: 1.23 (0.35), residues: 614 helix: 1.85 (0.25), residues: 416 sheet: -2.78 (1.08), residues: 20 loop : -1.25 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.019 0.002 TYR B 26 PHE 0.017 0.001 PHE B 55 TRP 0.025 0.002 TRP B 295 HIS 0.001 0.000 HIS I 2 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5190) covalent geometry : angle 1.14858 ( 7166) hydrogen bonds : bond 0.03325 ( 332) hydrogen bonds : angle 3.72709 ( 966) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 1.54362 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 861.48 seconds wall clock time: 15 minutes 35.30 seconds (935.30 seconds total)