Starting phenix.real_space_refine on Thu Jul 2 07:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uo1_64369/07_2026/9uo1_64369.map" } resolution = 2.9 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= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 5086 2.51 5 N 958 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7238 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2542 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 308} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 360 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2542 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 308} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 360 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 676 Unusual residues: {'76F': 3, 'CLR': 13, 'LPE': 1, 'P0E': 1, 'PLM': 6, 'ZWY': 2} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'76F:plan-3': 2, 'PLM:plan-1': 6} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 588 Unusual residues: {'76F': 1, 'CLR': 13, 'LPE': 1, 'P0E': 1, 'PLM': 6, 'ZWY': 2} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'PLM:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.34, per 1000 atoms: 0.19 Number of scatterers: 7238 At special positions: 0 Unit cell: (71.688, 79.928, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 8 15.00 O 1130 8.00 N 958 7.00 C 5086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 284 " distance=2.06 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 284 " 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 298.7 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 47 through 79 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.858A pdb=" N TYR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 173 through 202 Proline residue: A 184 - end of helix removed outlier: 3.786A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.566A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.193A pdb=" N GLN A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 318 Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.811A pdb=" N GLU B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 62 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 47 through 78 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.569A pdb=" N VAL C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.121A pdb=" N CYS C 163 " --> pdb=" O CYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 202 Proline residue: C 184 - end of helix removed outlier: 3.809A pdb=" N TYR C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.636A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 280 removed outlier: 4.269A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 289 through 318 Processing helix chain 'D' and resid 18 through 28 removed outlier: 3.793A pdb=" N GLU D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 62 440 hydrogen bonds defined for protein. 1311 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: 0.72 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 908 1.27 - 1.40: 1459 1.40 - 1.54: 4702 1.54 - 1.68: 303 1.68 - 1.81: 80 Bond restraints: 7452 Sorted by residual: bond pdb=" N 76F C 401 " pdb=" C5 76F C 401 " ideal model delta sigma weight residual 1.454 1.132 0.322 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N 76F A 401 " pdb=" C5 76F A 401 " ideal model delta sigma weight residual 1.454 1.134 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C21 76F C 401 " pdb=" C22 76F C 401 " ideal model delta sigma weight residual 1.330 1.547 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C21 76F A 401 " pdb=" C22 76F A 401 " ideal model delta sigma weight residual 1.330 1.546 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C40 76F A 401 " pdb=" C41 76F A 401 " ideal model delta sigma weight residual 1.330 1.544 -0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 7447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.51: 10225 13.51 - 27.03: 13 27.03 - 40.54: 0 40.54 - 54.06: 0 54.06 - 67.57: 2 Bond angle restraints: 10240 Sorted by residual: angle pdb=" N 76F C 401 " pdb=" C5 76F C 401 " pdb=" C4 76F C 401 " ideal model delta sigma weight residual 112.35 179.92 -67.57 3.00e+00 1.11e-01 5.07e+02 angle pdb=" N 76F A 401 " pdb=" C5 76F A 401 " pdb=" C4 76F A 401 " ideal model delta sigma weight residual 112.35 177.82 -65.47 3.00e+00 1.11e-01 4.76e+02 angle pdb=" O31 LPE C 405 " pdb=" P LPE C 405 " pdb=" O32 LPE C 405 " ideal model delta sigma weight residual 122.76 101.54 21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" O31 LPE A 404 " pdb=" P LPE A 404 " pdb=" O32 LPE A 404 " ideal model delta sigma weight residual 122.76 101.57 21.19 3.00e+00 1.11e-01 4.99e+01 angle pdb=" O1P 76F C 401 " pdb=" P 76F C 401 " pdb=" O2P 76F C 401 " ideal model delta sigma weight residual 119.76 100.95 18.81 3.00e+00 1.11e-01 3.93e+01 ... (remaining 10235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 5946 32.34 - 64.69: 257 64.69 - 97.03: 47 97.03 - 129.37: 16 129.37 - 161.72: 8 Dihedral angle restraints: 6274 sinusoidal: 4094 harmonic: 2180 Sorted by residual: dihedral pdb=" CB CYS C 32 " pdb=" SG CYS C 32 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual 93.00 -178.50 -88.50 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 32 " pdb=" SG CYS A 32 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 177.22 -84.22 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" C19 76F A 426 " pdb=" C20 76F A 426 " pdb=" C21 76F A 426 " pdb=" C22 76F A 426 " ideal model delta sinusoidal sigma weight residual 113.32 -84.96 -161.72 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1218 0.086 - 0.172: 49 0.172 - 0.258: 3 0.258 - 0.344: 0 0.344 - 0.430: 2 Chirality restraints: 1272 Sorted by residual: chirality pdb=" C2 76F A 426 " pdb=" C1 76F A 426 " pdb=" C3 76F A 426 " pdb=" O2 76F A 426 " both_signs ideal model delta sigma weight residual False -2.36 -2.79 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 76F A 402 " pdb=" C1 76F A 402 " pdb=" C3 76F A 402 " pdb=" O2 76F A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.79 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA ILE C 83 " pdb=" N ILE C 83 " pdb=" C ILE C 83 " pdb=" CB ILE C 83 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1269 not shown) Planarity restraints: 1016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 76F A 426 " 0.097 2.00e-02 2.50e+03 1.89e-01 3.57e+02 pdb=" C21 76F A 426 " -0.256 2.00e-02 2.50e+03 pdb=" C22 76F A 426 " 0.246 2.00e-02 2.50e+03 pdb=" C23 76F A 426 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 76F A 402 " -0.096 2.00e-02 2.50e+03 1.86e-01 3.45e+02 pdb=" C21 76F A 402 " 0.251 2.00e-02 2.50e+03 pdb=" C22 76F A 402 " -0.242 2.00e-02 2.50e+03 pdb=" C23 76F A 402 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 76F A 402 " -0.174 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" C18 76F A 402 " 0.186 2.00e-02 2.50e+03 pdb=" C19 76F A 402 " 0.156 2.00e-02 2.50e+03 pdb=" C20 76F A 402 " -0.167 2.00e-02 2.50e+03 ... (remaining 1013 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 782 2.75 - 3.29: 6983 3.29 - 3.83: 11530 3.83 - 4.36: 14330 4.36 - 4.90: 24688 Nonbonded interactions: 58313 Sorted by model distance: nonbonded pdb=" O LEU C 302 " pdb=" OG1 THR C 306 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 14 " pdb=" OE2 GLU B 23 " model vdw 2.344 3.040 nonbonded pdb=" O GLU A 20 " pdb=" OG1 THR A 24 " model vdw 2.345 3.040 nonbonded pdb=" O GLU C 20 " pdb=" OG1 THR C 24 " model vdw 2.362 3.040 nonbonded pdb=" O VAL D 47 " pdb=" OG SER D 51 " model vdw 2.375 3.040 ... (remaining 58308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 401 or resid 406 through 415 or (resid 417 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name O2 )) or (resid 418 \ through 419 and (name C1 or name C2 or name C3 or name C4 or name O2 )) or (resi \ d 420 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or nam \ e O2 )) or resid 421 or resid 423)) selection = (chain 'C' and (resid 2 through 401 or resid 406 through 415 or resid 417 or (re \ sid 418 through 419 and (name C1 or name C2 or name C3 or name C4 or name O2 )) \ or resid 420 or (resid 421 and (name C1 or name C2 or name C3 or name C4 or name \ O2 )) or resid 423)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 0.011 0.322 7459 Z= 0.571 Angle : 1.508 67.571 10244 Z= 0.574 Chirality : 0.041 0.430 1272 Planarity : 0.016 0.189 1016 Dihedral : 17.767 161.718 4856 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.62 % Allowed : 18.17 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 1.86 (0.30), residues: 740 helix: 1.89 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -0.84 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 13 TYR 0.019 0.002 TYR C 187 PHE 0.010 0.002 PHE C 127 TRP 0.010 0.001 TRP B 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.57 ( 7452) covalent geometry : angle 1.50772 / 0.57 (10240) SS BOND : bond 0.02253 / 1.18 ( 2) SS BOND : angle 1.90986 / 1.09 ( 4) hydrogen bonds : bond 0.08045 / 5.32 ( 440) hydrogen bonds : angle 4.78714 / 3.57 ( 1311) Misc. bond : bond 0.00064 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.148 Fit side-chains REVERT: A 323 LYS cc_start: 0.8141 (mptt) cc_final: 0.7350 (mtpt) REVERT: B 52 MET cc_start: 0.8487 (mmt) cc_final: 0.7397 (ttt) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.4506 time to fit residues: 38.0370 Evaluate side-chains 80 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 266 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125963 restraints weight = 7895.294| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.55 r_work: 0.3482 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7459 Z= 0.138 Angle : 0.566 7.142 10244 Z= 0.255 Chirality : 0.034 0.126 1272 Planarity : 0.004 0.047 1016 Dihedral : 15.556 175.591 3509 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 2.74 (0.30), residues: 740 helix: 2.51 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.41 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 149 TYR 0.015 0.001 TYR A 123 PHE 0.007 0.001 PHE A 127 TRP 0.007 0.001 TRP B 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7452) covalent geometry : angle 0.56554 / 0.25 (10240) SS BOND : bond 0.00191 / 0.10 ( 2) SS BOND : angle 1.26810 / 0.73 ( 4) hydrogen bonds : bond 0.05443 / 3.74 ( 440) hydrogen bonds : angle 4.02216 / 3.02 ( 1311) Misc. bond : bond 0.00007 / 0.00 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.157 Fit side-chains REVERT: A 323 LYS cc_start: 0.8250 (mptt) cc_final: 0.7477 (mtpt) REVERT: B 52 MET cc_start: 0.8638 (mmt) cc_final: 0.7539 (ttt) REVERT: C 23 LYS cc_start: 0.7470 (mttp) cc_final: 0.7149 (mttp) REVERT: C 323 LYS cc_start: 0.7930 (mptt) cc_final: 0.7127 (ttpt) outliers start: 14 outliers final: 6 residues processed: 91 average time/residue: 0.4469 time to fit residues: 43.0412 Evaluate side-chains 77 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122245 restraints weight = 7747.198| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.53 r_work: 0.3449 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7459 Z= 0.142 Angle : 0.563 6.792 10244 Z= 0.256 Chirality : 0.035 0.123 1272 Planarity : 0.004 0.052 1016 Dihedral : 14.484 155.505 3504 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.26 % Allowed : 15.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 2.95 (0.30), residues: 740 helix: 2.59 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.16 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 149 TYR 0.015 0.001 TYR A 123 PHE 0.008 0.001 PHE C 68 TRP 0.006 0.001 TRP B 36 HIS 0.005 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7452) covalent geometry : angle 0.56201 / 0.26 (10240) SS BOND : bond 0.00209 / 0.11 ( 2) SS BOND : angle 1.38427 / 0.79 ( 4) hydrogen bonds : bond 0.05470 / 3.75 ( 440) hydrogen bonds : angle 3.88991 / 2.91 ( 1311) Misc. bond : bond 0.00008 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.186 Fit side-chains REVERT: A 80 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 178 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7871 (mm110) REVERT: A 323 LYS cc_start: 0.8322 (mptt) cc_final: 0.7504 (mtpt) REVERT: B 52 MET cc_start: 0.8699 (mmt) cc_final: 0.7595 (ttt) REVERT: C 323 LYS cc_start: 0.8005 (mptt) cc_final: 0.7117 (ttpt) outliers start: 21 outliers final: 6 residues processed: 95 average time/residue: 0.4469 time to fit residues: 45.0754 Evaluate side-chains 84 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 289 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.153072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122946 restraints weight = 7921.052| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.57 r_work: 0.3436 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7459 Z= 0.127 Angle : 0.514 5.223 10244 Z= 0.236 Chirality : 0.034 0.123 1272 Planarity : 0.004 0.049 1016 Dihedral : 14.007 160.660 3504 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.11 % Allowed : 17.55 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.18 (0.30), residues: 740 helix: 2.75 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.09 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 149 TYR 0.017 0.001 TYR A 123 PHE 0.007 0.001 PHE A 127 TRP 0.007 0.001 TRP B 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7452) covalent geometry : angle 0.51388 / 0.24 (10240) SS BOND : bond 0.00187 / 0.10 ( 2) SS BOND : angle 1.19985 / 0.70 ( 4) hydrogen bonds : bond 0.05075 / 3.48 ( 440) hydrogen bonds : angle 3.74777 / 2.80 ( 1311) Misc. bond : bond 0.00010 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.234 Fit side-chains REVERT: A 9 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6422 (mmmt) REVERT: A 323 LYS cc_start: 0.8271 (mptt) cc_final: 0.7365 (mtpt) REVERT: B 52 MET cc_start: 0.8643 (mmt) cc_final: 0.7423 (ttt) REVERT: C 149 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8144 (ttm110) REVERT: C 178 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7772 (mm-40) REVERT: C 323 LYS cc_start: 0.8035 (mptt) cc_final: 0.7067 (ttpt) REVERT: D 23 GLU cc_start: 0.8438 (tt0) cc_final: 0.8227 (tt0) outliers start: 20 outliers final: 8 residues processed: 95 average time/residue: 0.4303 time to fit residues: 43.4384 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 289 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122379 restraints weight = 7866.510| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.56 r_work: 0.3432 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7459 Z= 0.124 Angle : 0.504 5.239 10244 Z= 0.233 Chirality : 0.034 0.125 1272 Planarity : 0.004 0.049 1016 Dihedral : 13.743 168.455 3504 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.88 % Allowed : 16.30 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.27 (0.30), residues: 740 helix: 2.83 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.07 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.017 0.001 TYR A 123 PHE 0.007 0.001 PHE A 127 TRP 0.007 0.001 TRP D 26 HIS 0.002 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7452) covalent geometry : angle 0.50373 / 0.23 (10240) SS BOND : bond 0.00170 / 0.09 ( 2) SS BOND : angle 1.16620 / 0.68 ( 4) hydrogen bonds : bond 0.05051 / 3.46 ( 440) hydrogen bonds : angle 3.71525 / 2.77 ( 1311) Misc. bond : bond 0.00013 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.254 Fit side-chains REVERT: A 7 GLN cc_start: 0.7897 (tt0) cc_final: 0.6884 (mm110) REVERT: A 9 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6451 (mmmt) REVERT: A 23 LYS cc_start: 0.6947 (mttp) cc_final: 0.6730 (mttp) REVERT: A 26 TYR cc_start: 0.8614 (m-80) cc_final: 0.7991 (m-10) REVERT: A 80 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 323 LYS cc_start: 0.8303 (mptt) cc_final: 0.7384 (mtpt) REVERT: B 52 MET cc_start: 0.8646 (mmt) cc_final: 0.7412 (ttt) REVERT: C 7 GLN cc_start: 0.7732 (tt0) cc_final: 0.6754 (mm110) REVERT: C 23 LYS cc_start: 0.7400 (mttp) cc_final: 0.7171 (mttp) REVERT: C 149 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8041 (ttm110) REVERT: C 323 LYS cc_start: 0.8020 (mptt) cc_final: 0.7057 (ttpt) REVERT: D 23 GLU cc_start: 0.8412 (tt0) cc_final: 0.8210 (tt0) outliers start: 25 outliers final: 13 residues processed: 104 average time/residue: 0.4346 time to fit residues: 48.1468 Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118941 restraints weight = 7918.126| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.61 r_work: 0.3390 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7459 Z= 0.155 Angle : 0.551 5.286 10244 Z= 0.255 Chirality : 0.035 0.123 1272 Planarity : 0.004 0.059 1016 Dihedral : 13.724 178.333 3504 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.95 % Allowed : 17.86 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.17 (0.30), residues: 740 helix: 2.78 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -0.17 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.018 0.002 TYR A 123 PHE 0.008 0.001 PHE C 138 TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 7452) covalent geometry : angle 0.55003 / 0.25 (10240) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 1.45648 / 0.84 ( 4) hydrogen bonds : bond 0.05544 / 3.80 ( 440) hydrogen bonds : angle 3.81008 / 2.85 ( 1311) Misc. bond : bond 0.00020 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.149 Fit side-chains REVERT: A 9 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6445 (mmmt) REVERT: A 80 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 323 LYS cc_start: 0.8312 (mptt) cc_final: 0.7352 (mtpt) REVERT: B 52 MET cc_start: 0.8601 (mmt) cc_final: 0.7351 (ttt) REVERT: C 7 GLN cc_start: 0.7701 (tt0) cc_final: 0.6786 (mm-40) REVERT: C 149 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8048 (ttm110) REVERT: C 323 LYS cc_start: 0.8063 (mptt) cc_final: 0.7217 (mtpt) REVERT: D 23 GLU cc_start: 0.8350 (tt0) cc_final: 0.8149 (tt0) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 0.4876 time to fit residues: 51.0918 Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118728 restraints weight = 7932.504| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.62 r_work: 0.3386 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7459 Z= 0.157 Angle : 0.539 5.305 10244 Z= 0.251 Chirality : 0.035 0.125 1272 Planarity : 0.004 0.049 1016 Dihedral : 13.619 169.964 3504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.26 % Allowed : 18.01 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.19 (0.30), residues: 740 helix: 2.75 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 44 TYR 0.018 0.002 TYR A 123 PHE 0.008 0.001 PHE A 127 TRP 0.008 0.001 TRP B 36 HIS 0.004 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7452) covalent geometry : angle 0.53818 / 0.25 (10240) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 1.40340 / 0.82 ( 4) hydrogen bonds : bond 0.05482 / 3.76 ( 440) hydrogen bonds : angle 3.85814 / 2.88 ( 1311) Misc. bond : bond 0.00024 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.195 Fit side-chains REVERT: A 9 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6483 (mmmt) REVERT: A 323 LYS cc_start: 0.8333 (mptt) cc_final: 0.7348 (mtpt) REVERT: B 52 MET cc_start: 0.8611 (mmt) cc_final: 0.7390 (ttt) REVERT: C 7 GLN cc_start: 0.7699 (tt0) cc_final: 0.6806 (mm110) REVERT: C 23 LYS cc_start: 0.7469 (mttp) cc_final: 0.7268 (mttp) REVERT: C 323 LYS cc_start: 0.8090 (mptt) cc_final: 0.7215 (mtpt) outliers start: 21 outliers final: 13 residues processed: 100 average time/residue: 0.4812 time to fit residues: 50.9275 Evaluate side-chains 99 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121853 restraints weight = 7852.074| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.55 r_work: 0.3465 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7459 Z= 0.126 Angle : 0.508 5.186 10244 Z= 0.238 Chirality : 0.034 0.123 1272 Planarity : 0.004 0.047 1016 Dihedral : 13.249 156.375 3504 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.48 % Allowed : 19.57 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.37 (0.31), residues: 740 helix: 2.88 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 0.04 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 44 TYR 0.017 0.001 TYR A 123 PHE 0.007 0.001 PHE A 127 TRP 0.007 0.001 TRP D 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7452) covalent geometry : angle 0.50745 / 0.24 (10240) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 1.24154 / 0.73 ( 4) hydrogen bonds : bond 0.05055 / 3.47 ( 440) hydrogen bonds : angle 3.77431 / 2.81 ( 1311) Misc. bond : bond 0.00017 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.239 Fit side-chains REVERT: A 9 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6479 (mmmt) REVERT: A 18 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 323 LYS cc_start: 0.8439 (mptt) cc_final: 0.7508 (mtpt) REVERT: B 52 MET cc_start: 0.8730 (mmt) cc_final: 0.7557 (ttt) REVERT: C 7 GLN cc_start: 0.7842 (tt0) cc_final: 0.6919 (mm110) REVERT: C 323 LYS cc_start: 0.8214 (mptt) cc_final: 0.7399 (mtpt) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.4532 time to fit residues: 47.5349 Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.0170 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122653 restraints weight = 7801.981| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.54 r_work: 0.3477 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7459 Z= 0.122 Angle : 0.513 7.626 10244 Z= 0.240 Chirality : 0.034 0.135 1272 Planarity : 0.004 0.050 1016 Dihedral : 12.896 156.290 3504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.64 % Allowed : 19.57 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.41 (0.31), residues: 740 helix: 2.94 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.00 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 13 TYR 0.017 0.001 TYR A 123 PHE 0.008 0.001 PHE A 127 TRP 0.006 0.001 TRP B 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7452) covalent geometry : angle 0.51256 / 0.24 (10240) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 1.16643 / 0.68 ( 4) hydrogen bonds : bond 0.04947 / 3.40 ( 440) hydrogen bonds : angle 3.76062 / 2.80 ( 1311) Misc. bond : bond 0.00016 / 0.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6503 (mmmt) REVERT: A 18 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 323 LYS cc_start: 0.8444 (mptt) cc_final: 0.7511 (mtpt) REVERT: B 52 MET cc_start: 0.8717 (mmt) cc_final: 0.7537 (ttt) REVERT: C 7 GLN cc_start: 0.7797 (tt0) cc_final: 0.6914 (mm110) REVERT: C 323 LYS cc_start: 0.8263 (mptt) cc_final: 0.7266 (ttpt) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.4420 time to fit residues: 46.2117 Evaluate side-chains 102 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110813 restraints weight = 8086.085| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.45 r_work: 0.3181 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7459 Z= 0.152 Angle : 0.542 5.896 10244 Z= 0.254 Chirality : 0.035 0.132 1272 Planarity : 0.005 0.078 1016 Dihedral : 12.991 155.562 3504 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.48 % Allowed : 20.34 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.29 (0.31), residues: 740 helix: 2.78 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 0.17 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 13 TYR 0.017 0.002 TYR A 123 PHE 0.009 0.001 PHE A 127 TRP 0.009 0.001 TRP D 36 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7452) covalent geometry : angle 0.54140 / 0.25 (10240) SS BOND : bond 0.00215 / 0.11 ( 2) SS BOND : angle 1.31806 / 0.77 ( 4) hydrogen bonds : bond 0.05371 / 3.69 ( 440) hydrogen bonds : angle 3.82596 / 2.85 ( 1311) Misc. bond : bond 0.00025 / 0.02 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.248 Fit side-chains REVERT: A 9 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6497 (mmmt) REVERT: A 323 LYS cc_start: 0.8360 (mptt) cc_final: 0.7433 (mtpt) REVERT: B 52 MET cc_start: 0.8746 (mmt) cc_final: 0.7561 (ttt) REVERT: C 7 GLN cc_start: 0.7772 (tt0) cc_final: 0.6905 (mm110) REVERT: C 323 LYS cc_start: 0.8239 (mptt) cc_final: 0.7231 (ttpt) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.4283 time to fit residues: 44.0733 Evaluate side-chains 101 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 19 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113816 restraints weight = 8090.968| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.44 r_work: 0.3185 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7459 Z= 0.128 Angle : 0.524 6.082 10244 Z= 0.247 Chirality : 0.034 0.123 1272 Planarity : 0.005 0.060 1016 Dihedral : 12.684 155.957 3504 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.17 % Allowed : 20.50 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: 3.40 (0.31), residues: 740 helix: 2.83 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.29 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 13 TYR 0.017 0.002 TYR A 123 PHE 0.008 0.001 PHE C 127 TRP 0.008 0.001 TRP B 26 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7452) covalent geometry : angle 0.52348 / 0.25 (10240) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 1.17408 / 0.69 ( 4) hydrogen bonds : bond 0.05067 / 3.48 ( 440) hydrogen bonds : angle 3.79740 / 2.83 ( 1311) Misc. bond : bond 0.00016 / 0.01 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.60 seconds wall clock time: 32 minutes 16.16 seconds (1936.16 seconds total)