Starting phenix.real_space_refine on Wed Feb 4 00:19:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddv_46781/02_2026/9ddv_46781.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 39 5.16 5 C 4944 2.51 5 N 1269 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7866 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2534 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 311} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Restraints were copied for chains: B, C Time building chain proxies: 1.71, per 1000 atoms: 0.22 Number of scatterers: 7866 At special positions: 0 Unit cell: (83.592, 88.128, 121.176, 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 39 16.00 O 1614 8.00 N 1269 7.00 C 4944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.02 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.02 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.02 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 298.0 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 27.9% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 39 through 60 removed outlier: 3.559A pdb=" N GLN A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 365 removed outlier: 3.506A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 3.559A pdb=" N GLN B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 365 removed outlier: 3.506A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 60 removed outlier: 3.559A pdb=" N GLN C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 365 removed outlier: 3.507A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AB3, first strand: chain 'C' and resid 86 through 87 211 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2421 1.34 - 1.46: 1951 1.46 - 1.58: 3464 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 7881 Sorted by residual: bond pdb=" N ILE C 129 " pdb=" CA ILE C 129 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.25e-02 6.40e+03 8.54e+00 bond pdb=" N VAL C 131 " pdb=" CA VAL C 131 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.50e+00 bond pdb=" N ILE A 129 " pdb=" CA ILE A 129 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.28e+00 bond pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.28e+00 bond pdb=" N ILE B 129 " pdb=" CA ILE B 129 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.25e-02 6.40e+03 8.22e+00 ... (remaining 7876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 9808 1.18 - 2.37: 729 2.37 - 3.55: 149 3.55 - 4.73: 24 4.73 - 5.91: 9 Bond angle restraints: 10719 Sorted by residual: angle pdb=" N LEU B 150 " pdb=" CA LEU B 150 " pdb=" C LEU B 150 " ideal model delta sigma weight residual 112.92 108.68 4.24 1.23e+00 6.61e-01 1.19e+01 angle pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" C LEU A 150 " ideal model delta sigma weight residual 112.92 108.73 4.19 1.23e+00 6.61e-01 1.16e+01 angle pdb=" N LEU C 150 " pdb=" CA LEU C 150 " pdb=" C LEU C 150 " ideal model delta sigma weight residual 112.92 108.73 4.19 1.23e+00 6.61e-01 1.16e+01 angle pdb=" N ILE A 129 " pdb=" CA ILE A 129 " pdb=" C ILE A 129 " ideal model delta sigma weight residual 113.00 108.78 4.22 1.30e+00 5.92e-01 1.05e+01 angle pdb=" N ILE C 129 " pdb=" CA ILE C 129 " pdb=" C ILE C 129 " ideal model delta sigma weight residual 113.00 108.79 4.21 1.30e+00 5.92e-01 1.05e+01 ... (remaining 10714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4347 17.50 - 35.00: 276 35.00 - 52.50: 81 52.50 - 69.99: 9 69.99 - 87.49: 6 Dihedral angle restraints: 4719 sinusoidal: 1902 harmonic: 2817 Sorted by residual: dihedral pdb=" CB CYS C 270 " pdb=" SG CYS C 270 " pdb=" SG CYS C 279 " pdb=" CB CYS C 279 " ideal model delta sinusoidal sigma weight residual -86.00 -146.32 60.32 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS A 270 " pdb=" SG CYS A 270 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual -86.00 -146.30 60.30 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual -86.00 -146.28 60.28 1 1.00e+01 1.00e-02 4.84e+01 ... (remaining 4716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 796 0.041 - 0.081: 278 0.081 - 0.122: 125 0.122 - 0.162: 19 0.162 - 0.203: 9 Chirality restraints: 1227 Sorted by residual: chirality pdb=" CA ILE C 129 " pdb=" N ILE C 129 " pdb=" C ILE C 129 " pdb=" CB ILE C 129 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE B 129 " pdb=" N ILE B 129 " pdb=" C ILE B 129 " pdb=" CB ILE B 129 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A 129 " pdb=" N ILE A 129 " pdb=" C ILE A 129 " pdb=" CB ILE A 129 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1224 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 324 " 0.240 9.50e-02 1.11e+02 1.08e-01 7.12e+00 pdb=" NE ARG B 324 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 324 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 324 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 324 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 324 " 0.240 9.50e-02 1.11e+02 1.08e-01 7.12e+00 pdb=" NE ARG C 324 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 324 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 324 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 324 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 324 " -0.240 9.50e-02 1.11e+02 1.08e-01 7.10e+00 pdb=" NE ARG A 324 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 324 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 324 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 324 " -0.008 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1211 2.76 - 3.29: 7446 3.29 - 3.83: 13344 3.83 - 4.36: 17212 4.36 - 4.90: 28434 Nonbonded interactions: 67647 Sorted by model distance: nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.221 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.221 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.221 3.040 nonbonded pdb=" O GLU A 103 " pdb=" O HOH A 601 " model vdw 2.242 3.040 nonbonded pdb=" O PRO B 101 " pdb=" O HOH B 601 " model vdw 2.260 3.040 ... (remaining 67642 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.670 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.050 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.042 7902 Z= 0.271 Angle : 0.711 5.913 10767 Z= 0.432 Chirality : 0.051 0.203 1227 Planarity : 0.007 0.108 1347 Dihedral : 12.863 87.491 2880 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.03 (0.26), residues: 975 helix: 1.24 (0.35), residues: 213 sheet: -0.35 (0.28), residues: 324 loop : -0.24 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.018 0.002 TYR B 283 PHE 0.011 0.001 PHE B 252 TRP 0.008 0.001 TRP B 361 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 7881) covalent geometry : angle 0.70609 (10719) SS BOND : bond 0.00465 ( 15) SS BOND : angle 1.52342 ( 30) hydrogen bonds : bond 0.18908 ( 211) hydrogen bonds : angle 6.20143 ( 543) link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 1.37570 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 87 THR cc_start: 0.8239 (p) cc_final: 0.7971 (m) REVERT: A 278 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 282 LYS cc_start: 0.7687 (tttp) cc_final: 0.7482 (tptp) REVERT: A 284 SER cc_start: 0.8259 (t) cc_final: 0.8017 (p) REVERT: B 149 MET cc_start: 0.8700 (mmp) cc_final: 0.8413 (tpp) REVERT: B 335 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8153 (tttt) REVERT: C 284 SER cc_start: 0.7911 (t) cc_final: 0.7710 (t) REVERT: C 312 THR cc_start: 0.8055 (p) cc_final: 0.7853 (t) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.5917 time to fit residues: 128.9483 Evaluate side-chains 184 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 300 ASN B 267 ASN B 300 ASN C 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113942 restraints weight = 10350.554| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.82 r_work: 0.3351 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7902 Z= 0.162 Angle : 0.566 5.973 10767 Z= 0.300 Chirality : 0.046 0.172 1227 Planarity : 0.005 0.036 1347 Dihedral : 6.095 52.564 1185 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 8.73 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.10 (0.27), residues: 975 helix: 0.87 (0.35), residues: 249 sheet: -0.35 (0.28), residues: 324 loop : -0.23 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.019 0.002 TYR A 98 PHE 0.010 0.001 PHE A 239 TRP 0.008 0.001 TRP A 268 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7881) covalent geometry : angle 0.56146 (10719) SS BOND : bond 0.00427 ( 15) SS BOND : angle 1.09741 ( 30) hydrogen bonds : bond 0.04860 ( 211) hydrogen bonds : angle 4.90933 ( 543) link_NAG-ASN : bond 0.00438 ( 6) link_NAG-ASN : angle 1.33134 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 LYS cc_start: 0.8086 (tttp) cc_final: 0.7866 (tttp) REVERT: B 96 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6509 (tm-30) REVERT: B 149 MET cc_start: 0.8860 (mmp) cc_final: 0.8655 (mmm) REVERT: C 150 LEU cc_start: 0.8190 (mt) cc_final: 0.7906 (mm) outliers start: 12 outliers final: 4 residues processed: 197 average time/residue: 0.5581 time to fit residues: 116.2139 Evaluate side-chains 192 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain C residue 191 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.0970 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 267 ASN A 300 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 = 0.3629 r_free = 0.3629 target = 0.123585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110720 restraints weight = 10287.935| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.76 r_work: 0.3367 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7902 Z= 0.122 Angle : 0.522 7.606 10767 Z= 0.273 Chirality : 0.046 0.236 1227 Planarity : 0.004 0.036 1347 Dihedral : 5.920 58.226 1185 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.97 % Allowed : 11.76 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.20 (0.27), residues: 975 helix: 1.60 (0.36), residues: 231 sheet: -0.41 (0.27), residues: 342 loop : -0.07 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 324 TYR 0.017 0.002 TYR A 98 PHE 0.008 0.001 PHE A 357 TRP 0.007 0.001 TRP A 268 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7881) covalent geometry : angle 0.50929 (10719) SS BOND : bond 0.00325 ( 15) SS BOND : angle 0.94657 ( 30) hydrogen bonds : bond 0.04116 ( 211) hydrogen bonds : angle 4.76203 ( 543) link_NAG-ASN : bond 0.00902 ( 6) link_NAG-ASN : angle 2.60784 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7377 (pt0) cc_final: 0.7174 (pt0) REVERT: B 96 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6448 (tm-30) REVERT: B 97 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 150 LEU cc_start: 0.8152 (mt) cc_final: 0.7750 (mm) outliers start: 8 outliers final: 4 residues processed: 199 average time/residue: 0.5825 time to fit residues: 122.4326 Evaluate side-chains 195 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 284 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN B 267 ASN B 300 ASN C 201 ASN C 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114183 restraints weight = 10482.276| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.86 r_work: 0.3344 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7902 Z= 0.137 Angle : 0.520 5.855 10767 Z= 0.273 Chirality : 0.045 0.166 1227 Planarity : 0.004 0.038 1347 Dihedral : 5.417 52.208 1185 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.45 % Allowed : 13.33 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.32 (0.27), residues: 975 helix: 1.60 (0.36), residues: 231 sheet: -0.46 (0.27), residues: 312 loop : 0.13 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 324 TYR 0.018 0.002 TYR A 98 PHE 0.009 0.001 PHE B 239 TRP 0.008 0.001 TRP A 268 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7881) covalent geometry : angle 0.51458 (10719) SS BOND : bond 0.00353 ( 15) SS BOND : angle 0.93436 ( 30) hydrogen bonds : bond 0.04044 ( 211) hydrogen bonds : angle 4.74694 ( 543) link_NAG-ASN : bond 0.00582 ( 6) link_NAG-ASN : angle 1.65128 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7399 (pt0) cc_final: 0.7196 (pt0) REVERT: B 96 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6513 (tm-30) REVERT: B 208 PHE cc_start: 0.8492 (m-10) cc_final: 0.8166 (m-80) REVERT: C 150 LEU cc_start: 0.8098 (mt) cc_final: 0.7799 (mm) outliers start: 12 outliers final: 6 residues processed: 198 average time/residue: 0.5982 time to fit residues: 125.0845 Evaluate side-chains 196 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain C residue 191 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 94 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 70 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 300 ASN B 152 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 = 0.3637 r_free = 0.3637 target = 0.127139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113912 restraints weight = 10425.470| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.84 r_work: 0.3356 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7902 Z= 0.128 Angle : 0.501 5.811 10767 Z= 0.264 Chirality : 0.045 0.163 1227 Planarity : 0.004 0.043 1347 Dihedral : 5.164 52.214 1185 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 14.30 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.36 (0.27), residues: 975 helix: 1.64 (0.37), residues: 231 sheet: -0.40 (0.27), residues: 312 loop : 0.14 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.018 0.002 TYR A 98 PHE 0.008 0.001 PHE B 239 TRP 0.007 0.001 TRP C 93 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7881) covalent geometry : angle 0.49522 (10719) SS BOND : bond 0.00328 ( 15) SS BOND : angle 0.89860 ( 30) hydrogen bonds : bond 0.03829 ( 211) hydrogen bonds : angle 4.73011 ( 543) link_NAG-ASN : bond 0.00452 ( 6) link_NAG-ASN : angle 1.66031 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7405 (pt0) cc_final: 0.7188 (pt0) REVERT: B 96 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6517 (tm-30) REVERT: B 97 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 208 PHE cc_start: 0.8471 (m-10) cc_final: 0.8084 (m-80) REVERT: C 46 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7457 (mtp-110) REVERT: C 66 SER cc_start: 0.8276 (m) cc_final: 0.8052 (m) REVERT: C 150 LEU cc_start: 0.8076 (mt) cc_final: 0.7781 (mm) REVERT: C 278 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7348 (mm-30) outliers start: 13 outliers final: 7 residues processed: 202 average time/residue: 0.6138 time to fit residues: 130.8682 Evaluate side-chains 198 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 87 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 152 ASN B 267 ASN B 300 ASN C 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113210 restraints weight = 10387.207| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.86 r_work: 0.3336 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7902 Z= 0.172 Angle : 0.539 5.921 10767 Z= 0.282 Chirality : 0.046 0.170 1227 Planarity : 0.004 0.040 1347 Dihedral : 5.256 53.059 1185 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 14.91 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.30 (0.27), residues: 975 helix: 1.48 (0.37), residues: 231 sheet: -0.37 (0.27), residues: 312 loop : 0.09 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.020 0.002 TYR A 98 PHE 0.010 0.001 PHE B 239 TRP 0.008 0.001 TRP A 268 HIS 0.002 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7881) covalent geometry : angle 0.53467 (10719) SS BOND : bond 0.00407 ( 15) SS BOND : angle 0.96368 ( 30) hydrogen bonds : bond 0.04233 ( 211) hydrogen bonds : angle 4.79908 ( 543) link_NAG-ASN : bond 0.00442 ( 6) link_NAG-ASN : angle 1.52057 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7685 (ptt90) REVERT: B 69 GLU cc_start: 0.7426 (pt0) cc_final: 0.7214 (pt0) REVERT: B 96 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 97 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7689 (mt-10) REVERT: B 208 PHE cc_start: 0.8483 (m-10) cc_final: 0.8090 (m-80) REVERT: C 46 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7531 (mtp-110) REVERT: C 66 SER cc_start: 0.8267 (m) cc_final: 0.8052 (m) REVERT: C 150 LEU cc_start: 0.8087 (mt) cc_final: 0.7864 (mm) REVERT: C 278 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7374 (mm-30) REVERT: C 360 ASP cc_start: 0.7292 (m-30) cc_final: 0.6943 (m-30) outliers start: 21 outliers final: 8 residues processed: 206 average time/residue: 0.6047 time to fit residues: 131.4091 Evaluate side-chains 207 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 300 ASN B 152 ASN B 300 ASN C 152 ASN C 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113166 restraints weight = 10434.841| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3331 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7902 Z= 0.179 Angle : 0.552 6.123 10767 Z= 0.287 Chirality : 0.046 0.183 1227 Planarity : 0.004 0.040 1347 Dihedral : 5.230 54.307 1185 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.30 % Allowed : 15.27 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.27 (0.27), residues: 975 helix: 1.43 (0.37), residues: 231 sheet: -0.37 (0.27), residues: 312 loop : 0.08 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 324 TYR 0.019 0.002 TYR A 98 PHE 0.010 0.001 PHE B 239 TRP 0.008 0.001 TRP A 268 HIS 0.002 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7881) covalent geometry : angle 0.54185 (10719) SS BOND : bond 0.00416 ( 15) SS BOND : angle 0.96999 ( 30) hydrogen bonds : bond 0.04319 ( 211) hydrogen bonds : angle 4.82772 ( 543) link_NAG-ASN : bond 0.01026 ( 6) link_NAG-ASN : angle 2.45404 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7708 (ptt90) REVERT: B 69 GLU cc_start: 0.7431 (pt0) cc_final: 0.7218 (pt0) REVERT: B 96 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6549 (tm-30) REVERT: B 97 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7688 (mt-10) REVERT: B 208 PHE cc_start: 0.8471 (m-10) cc_final: 0.8018 (m-80) REVERT: B 324 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7170 (ttm-80) REVERT: C 66 SER cc_start: 0.8274 (m) cc_final: 0.8064 (m) REVERT: C 278 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7364 (mm-30) REVERT: C 360 ASP cc_start: 0.7303 (m-30) cc_final: 0.6962 (m-30) outliers start: 19 outliers final: 10 residues processed: 204 average time/residue: 0.5926 time to fit residues: 127.7215 Evaluate side-chains 204 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 79 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 56 optimal weight: 0.3980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 300 ASN B 267 ASN B 300 ASN C 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114707 restraints weight = 10470.496| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.84 r_work: 0.3355 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7902 Z= 0.116 Angle : 0.503 5.784 10767 Z= 0.265 Chirality : 0.045 0.208 1227 Planarity : 0.004 0.042 1347 Dihedral : 5.105 55.361 1185 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.58 % Allowed : 16.24 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.36 (0.27), residues: 975 helix: 1.62 (0.37), residues: 231 sheet: -0.35 (0.27), residues: 312 loop : 0.09 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 324 TYR 0.017 0.002 TYR A 98 PHE 0.007 0.001 PHE B 56 TRP 0.007 0.001 TRP B 93 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7881) covalent geometry : angle 0.49675 (10719) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.88215 ( 30) hydrogen bonds : bond 0.03731 ( 211) hydrogen bonds : angle 4.74981 ( 543) link_NAG-ASN : bond 0.00736 ( 6) link_NAG-ASN : angle 1.76988 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7401 (pt0) cc_final: 0.7184 (pt0) REVERT: B 96 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6518 (tm-30) REVERT: B 208 PHE cc_start: 0.8461 (m-10) cc_final: 0.8007 (m-80) REVERT: C 66 SER cc_start: 0.8266 (m) cc_final: 0.8052 (m) REVERT: C 278 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7365 (mm-30) REVERT: C 360 ASP cc_start: 0.7288 (m-30) cc_final: 0.6957 (m-30) outliers start: 13 outliers final: 6 residues processed: 194 average time/residue: 0.6229 time to fit residues: 127.2946 Evaluate side-chains 196 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 201 ASN B 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114153 restraints weight = 10341.745| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.85 r_work: 0.3345 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7902 Z= 0.140 Angle : 0.515 5.793 10767 Z= 0.272 Chirality : 0.045 0.165 1227 Planarity : 0.004 0.044 1347 Dihedral : 5.085 55.705 1185 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 15.88 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.35 (0.27), residues: 975 helix: 1.56 (0.37), residues: 231 sheet: -0.32 (0.27), residues: 312 loop : 0.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 324 TYR 0.020 0.002 TYR A 98 PHE 0.008 0.001 PHE B 239 TRP 0.007 0.001 TRP B 93 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7881) covalent geometry : angle 0.50877 (10719) SS BOND : bond 0.00345 ( 15) SS BOND : angle 0.92479 ( 30) hydrogen bonds : bond 0.03871 ( 211) hydrogen bonds : angle 4.77384 ( 543) link_NAG-ASN : bond 0.00411 ( 6) link_NAG-ASN : angle 1.66855 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7629 (ptt90) REVERT: B 69 GLU cc_start: 0.7433 (pt0) cc_final: 0.7219 (pt0) REVERT: B 96 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6542 (tm-30) REVERT: B 208 PHE cc_start: 0.8461 (m-10) cc_final: 0.7988 (m-80) REVERT: B 324 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7298 (ttm-80) REVERT: C 66 SER cc_start: 0.8267 (m) cc_final: 0.8051 (m) REVERT: C 278 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 360 ASP cc_start: 0.7286 (m-30) cc_final: 0.6954 (m-30) outliers start: 14 outliers final: 8 residues processed: 197 average time/residue: 0.5718 time to fit residues: 118.9163 Evaluate side-chains 200 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 19 optimal weight: 0.0870 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 300 ASN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114571 restraints weight = 10416.686| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.86 r_work: 0.3355 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7902 Z= 0.123 Angle : 0.513 5.860 10767 Z= 0.269 Chirality : 0.045 0.196 1227 Planarity : 0.004 0.043 1347 Dihedral : 5.064 56.407 1185 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.09 % Allowed : 16.85 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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 (0.27), residues: 975 helix: 1.61 (0.37), residues: 231 sheet: -0.29 (0.28), residues: 312 loop : 0.10 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 324 TYR 0.019 0.002 TYR A 98 PHE 0.007 0.001 PHE B 239 TRP 0.008 0.001 TRP B 93 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7881) covalent geometry : angle 0.50627 (10719) SS BOND : bond 0.00306 ( 15) SS BOND : angle 0.89727 ( 30) hydrogen bonds : bond 0.03690 ( 211) hydrogen bonds : angle 4.74194 ( 543) link_NAG-ASN : bond 0.00971 ( 6) link_NAG-ASN : angle 1.91841 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7406 (pt0) cc_final: 0.7186 (pt0) REVERT: B 96 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6508 (tm-30) REVERT: B 208 PHE cc_start: 0.8450 (m-10) cc_final: 0.7984 (m-80) REVERT: C 66 SER cc_start: 0.8259 (m) cc_final: 0.8044 (m) outliers start: 9 outliers final: 7 residues processed: 198 average time/residue: 0.5503 time to fit residues: 115.0903 Evaluate side-chains 199 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN B 152 ASN B 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113887 restraints weight = 10460.635| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.86 r_work: 0.3349 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7902 Z= 0.133 Angle : 0.513 5.802 10767 Z= 0.271 Chirality : 0.045 0.163 1227 Planarity : 0.004 0.044 1347 Dihedral : 5.032 56.762 1185 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.82 % Allowed : 16.00 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.40 (0.27), residues: 975 helix: 1.61 (0.37), residues: 231 sheet: -0.28 (0.28), residues: 312 loop : 0.11 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 324 TYR 0.022 0.002 TYR A 98 PHE 0.008 0.001 PHE B 239 TRP 0.008 0.001 TRP B 93 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7881) covalent geometry : angle 0.50718 (10719) SS BOND : bond 0.00330 ( 15) SS BOND : angle 0.98794 ( 30) hydrogen bonds : bond 0.03731 ( 211) hydrogen bonds : angle 4.74909 ( 543) link_NAG-ASN : bond 0.00401 ( 6) link_NAG-ASN : angle 1.56562 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.83 seconds wall clock time: 59 minutes 18.46 seconds (3558.46 seconds total)