Starting phenix.real_space_refine on Fri Aug 22 19:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9etm_19944/08_2025/9etm_19944.map" } resolution = 3.35 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= 0.000 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 32 5.16 5 C 4810 2.51 5 N 1219 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7404 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 304 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "C" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2207 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 304 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "B" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2207 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.19 Number of scatterers: 7404 At special positions: 0 Unit cell: (94.581, 133.083, 95.418, 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 32 16.00 P 5 15.00 O 1338 8.00 N 1219 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 256 " distance=2.04 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 256 " distance=2.04 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 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 303.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 34.8% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'G' and resid 7 through 16 removed outlier: 4.078A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 14 " --> pdb=" O ILE G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 41 Processing helix chain 'I' and resid 11 through 45 removed outlier: 4.114A pdb=" N GLN I 15 " --> pdb=" O PRO I 11 " (cutoff:3.500A) Proline residue: I 40 - end of helix Processing helix chain 'E' and resid 10 through 38 removed outlier: 4.304A pdb=" N GLY E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'C' and resid 78 through 104 Processing helix chain 'C' and resid 104 through 123 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'H' and resid 8 through 16 removed outlier: 3.989A pdb=" N SER H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE H 14 " --> pdb=" O ILE H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 41 Processing helix chain 'J' and resid 11 through 45 removed outlier: 4.133A pdb=" N GLN J 15 " --> pdb=" O PRO J 11 " (cutoff:3.500A) Proline residue: J 40 - end of helix Processing helix chain 'F' and resid 10 through 38 removed outlier: 4.321A pdb=" N GLY F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'D' and resid 78 through 104 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 90 removed outlier: 6.144A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 161 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 90 removed outlier: 6.201A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 161 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1530 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: 0.80 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: 1.20 - 1.33: 1388 1.33 - 1.45: 1907 1.45 - 1.58: 4206 1.58 - 1.70: 10 1.70 - 1.83: 54 Bond restraints: 7565 Sorted by residual: bond pdb=" CG LEU A 295 " pdb=" CD1 LEU A 295 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.38e-01 bond pdb=" CG LEU A 311 " pdb=" CD2 LEU A 311 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.92e-01 bond pdb=" CG LEU B 295 " pdb=" CD1 LEU B 295 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.70e-01 bond pdb=" CB GLU B 270 " pdb=" CG GLU B 270 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.68e-01 bond pdb=" CG LEU B 311 " pdb=" CD2 LEU B 311 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.46e-01 ... (remaining 7560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 9847 1.48 - 2.96: 312 2.96 - 4.44: 47 4.44 - 5.93: 14 5.93 - 7.41: 1 Bond angle restraints: 10221 Sorted by residual: angle pdb=" N PHE G 40 " pdb=" CA PHE G 40 " pdb=" C PHE G 40 " ideal model delta sigma weight residual 112.87 117.03 -4.16 1.20e+00 6.94e-01 1.20e+01 angle pdb=" N GLY A 309 " pdb=" CA GLY A 309 " pdb=" C GLY A 309 " ideal model delta sigma weight residual 113.18 107.72 5.46 2.37e+00 1.78e-01 5.30e+00 angle pdb=" N TRP F 24 " pdb=" CA TRP F 24 " pdb=" C TRP F 24 " ideal model delta sigma weight residual 112.23 115.12 -2.89 1.26e+00 6.30e-01 5.26e+00 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 109.81 114.77 -4.96 2.21e+00 2.05e-01 5.04e+00 angle pdb=" CA CYS B 256 " pdb=" CB CYS B 256 " pdb=" SG CYS B 256 " ideal model delta sigma weight residual 114.40 119.50 -5.10 2.30e+00 1.89e-01 4.92e+00 ... (remaining 10216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 4387 34.35 - 68.70: 109 68.70 - 103.04: 15 103.04 - 137.39: 10 137.39 - 171.74: 2 Dihedral angle restraints: 4523 sinusoidal: 1877 harmonic: 2646 Sorted by residual: dihedral pdb=" CA LEU B 311 " pdb=" C LEU B 311 " pdb=" N GLU B 312 " pdb=" CA GLU B 312 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP A 305 " pdb=" C TRP A 305 " pdb=" N GLN A 306 " pdb=" CA GLN A 306 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 318 " pdb=" C LEU A 318 " pdb=" N PRO A 319 " pdb=" CA PRO A 319 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 4520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1016 0.072 - 0.143: 108 0.143 - 0.215: 2 0.215 - 0.286: 0 0.286 - 0.358: 1 Chirality restraints: 1127 Sorted by residual: chirality pdb=" CA PHE G 40 " pdb=" N PHE G 40 " pdb=" C PHE G 40 " pdb=" CB PHE G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ILE A 99 " pdb=" N ILE A 99 " pdb=" C ILE A 99 " pdb=" CB ILE A 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1124 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 113 " -0.269 9.50e-02 1.11e+02 1.21e-01 1.04e+01 pdb=" NE ARG D 113 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 113 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 113 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 113 " 0.246 9.50e-02 1.11e+02 1.10e-01 7.90e+00 pdb=" NE ARG C 113 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 113 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 113 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 113 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 286 " -0.005 2.00e-02 2.50e+03 1.32e-02 3.49e+00 pdb=" CG TYR B 286 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 286 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 286 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 286 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 286 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 286 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR B 286 " -0.022 2.00e-02 2.50e+03 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2732 2.88 - 3.39: 7049 3.39 - 3.89: 11692 3.89 - 4.40: 13093 4.40 - 4.90: 23915 Nonbonded interactions: 58481 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" OE1 GLN A 259 " model vdw 2.377 3.040 nonbonded pdb=" OH TYR B 257 " pdb=" OE1 GLN B 259 " model vdw 2.401 3.040 nonbonded pdb=" NH1 ARG B 110 " pdb=" OD1 ASP B 133 " model vdw 2.440 3.120 nonbonded pdb=" O VAL C 107 " pdb=" OG1 THR C 111 " model vdw 2.443 3.040 nonbonded pdb=" O2 PLC C 401 " pdb=" O3 PLC C 401 " model vdw 2.444 2.432 ... (remaining 58476 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' selection = (chain 'B' and resid 55 through 344) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 2.850 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.003 0.026 7567 Z= 0.129 Angle : 0.646 7.406 10225 Z= 0.361 Chirality : 0.044 0.358 1127 Planarity : 0.007 0.121 1286 Dihedral : 17.420 171.741 2817 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: -0.09 (0.27), residues: 908 helix: -0.30 (0.26), residues: 282 sheet: 0.55 (0.26), residues: 394 loop : -0.49 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG D 113 TYR 0.022 0.006 TYR B 286 PHE 0.016 0.003 PHE B 127 TRP 0.026 0.004 TRP A 305 HIS 0.007 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7565) covalent geometry : angle 0.64288 (10221) SS BOND : bond 0.00548 ( 2) SS BOND : angle 3.34497 ( 4) hydrogen bonds : bond 0.18133 ( 531) hydrogen bonds : angle 8.33029 ( 1530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.279 Fit side-chains REVERT: C 115 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7667 (tm-30) REVERT: D 115 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 155 LYS cc_start: 0.7458 (mttp) cc_final: 0.7038 (mtpt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0712 time to fit residues: 18.6515 Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 GLN A 97 HIS A 254 HIS J 8 GLN B 97 HIS B 254 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.215269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.177204 restraints weight = 9117.204| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.69 r_work: 0.4214 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7567 Z= 0.251 Angle : 0.824 16.376 10225 Z= 0.423 Chirality : 0.050 0.220 1127 Planarity : 0.005 0.054 1286 Dihedral : 17.020 168.066 1171 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.36 % Allowed : 10.98 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.40 (0.28), residues: 908 helix: 0.91 (0.28), residues: 302 sheet: 0.31 (0.25), residues: 394 loop : -0.45 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 110 TYR 0.017 0.002 TYR B 237 PHE 0.024 0.003 PHE I 29 TRP 0.011 0.002 TRP E 53 HIS 0.008 0.002 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 7565) covalent geometry : angle 0.82145 (10221) SS BOND : bond 0.00168 ( 2) SS BOND : angle 3.60372 ( 4) hydrogen bonds : bond 0.04250 ( 531) hydrogen bonds : angle 6.03519 ( 1530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.269 Fit side-chains REVERT: A 298 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: D 115 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 155 LYS cc_start: 0.7546 (mttp) cc_final: 0.7056 (mtpt) REVERT: B 298 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.6794 (mtm-85) outliers start: 26 outliers final: 19 residues processed: 153 average time/residue: 0.0772 time to fit residues: 16.0253 Evaluate side-chains 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 8 GLN A 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.215074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.177687 restraints weight = 9120.756| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.64 r_work: 0.4219 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7567 Z= 0.211 Angle : 0.741 11.394 10225 Z= 0.382 Chirality : 0.047 0.172 1127 Planarity : 0.005 0.043 1286 Dihedral : 16.300 165.153 1171 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.62 % Allowed : 13.57 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.52 (0.28), residues: 908 helix: 1.09 (0.28), residues: 308 sheet: 0.30 (0.26), residues: 392 loop : -0.41 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.016 0.002 TYR B 115 PHE 0.014 0.002 PHE I 29 TRP 0.012 0.001 TRP D 94 HIS 0.004 0.001 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7565) covalent geometry : angle 0.73936 (10221) SS BOND : bond 0.00087 ( 2) SS BOND : angle 2.81082 ( 4) hydrogen bonds : bond 0.03663 ( 531) hydrogen bonds : angle 5.82577 ( 1530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.173 Fit side-chains REVERT: I 7 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8480 (p) REVERT: C 115 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 116 MET cc_start: 0.7540 (tpp) cc_final: 0.7320 (tpp) REVERT: J 7 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (p) REVERT: D 115 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.0777 time to fit residues: 15.2574 Evaluate side-chains 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.215458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.177130 restraints weight = 9259.060| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.71 r_work: 0.4209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7567 Z= 0.202 Angle : 0.731 10.443 10225 Z= 0.372 Chirality : 0.046 0.188 1127 Planarity : 0.005 0.043 1286 Dihedral : 15.966 165.104 1171 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.39 % Allowed : 13.82 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.69 (0.28), residues: 908 helix: 1.31 (0.28), residues: 310 sheet: 0.40 (0.26), residues: 386 loop : -0.43 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.017 0.002 TYR A 115 PHE 0.014 0.002 PHE C 109 TRP 0.012 0.001 TRP D 94 HIS 0.004 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7565) covalent geometry : angle 0.72928 (10221) SS BOND : bond 0.00034 ( 2) SS BOND : angle 2.51427 ( 4) hydrogen bonds : bond 0.03436 ( 531) hydrogen bonds : angle 5.68181 ( 1530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.315 Fit side-chains REVERT: I 7 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 115 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7694 (tm-30) REVERT: J 7 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8436 (p) REVERT: D 115 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 298 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.6586 (mtm-85) outliers start: 34 outliers final: 28 residues processed: 149 average time/residue: 0.0794 time to fit residues: 16.5435 Evaluate side-chains 154 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.208264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.171444 restraints weight = 8841.616| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 2.45 r_work: 0.4222 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7567 Z= 0.223 Angle : 0.744 10.736 10225 Z= 0.378 Chirality : 0.046 0.174 1127 Planarity : 0.005 0.045 1286 Dihedral : 15.858 164.606 1171 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.43 % Allowed : 13.57 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.65 (0.28), residues: 908 helix: 1.34 (0.28), residues: 310 sheet: 0.29 (0.26), residues: 386 loop : -0.42 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 110 TYR 0.018 0.002 TYR A 115 PHE 0.022 0.002 PHE C 109 TRP 0.012 0.001 TRP D 94 HIS 0.004 0.002 HIS J 45 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 7565) covalent geometry : angle 0.74196 (10221) SS BOND : bond 0.00042 ( 2) SS BOND : angle 2.59584 ( 4) hydrogen bonds : bond 0.03427 ( 531) hydrogen bonds : angle 5.71015 ( 1530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.286 Fit side-chains REVERT: C 115 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7568 (tm-30) REVERT: D 115 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 298 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.6509 (mtm-85) outliers start: 42 outliers final: 32 residues processed: 158 average time/residue: 0.0704 time to fit residues: 15.8737 Evaluate side-chains 160 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.216417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.178956 restraints weight = 9182.849| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 2.67 r_work: 0.4239 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7567 Z= 0.146 Angle : 0.692 12.136 10225 Z= 0.346 Chirality : 0.045 0.165 1127 Planarity : 0.004 0.045 1286 Dihedral : 15.314 164.783 1171 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.62 % Allowed : 16.28 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.99 (0.29), residues: 908 helix: 1.65 (0.28), residues: 310 sheet: 0.46 (0.27), residues: 386 loop : -0.26 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 110 TYR 0.020 0.001 TYR B 115 PHE 0.019 0.002 PHE I 29 TRP 0.014 0.001 TRP D 94 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7565) covalent geometry : angle 0.69095 (10221) SS BOND : bond 0.00079 ( 2) SS BOND : angle 1.97440 ( 4) hydrogen bonds : bond 0.03034 ( 531) hydrogen bonds : angle 5.51210 ( 1530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.323 Fit side-chains REVERT: C 115 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 247 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7576 (t) REVERT: D 115 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 247 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7570 (t) outliers start: 28 outliers final: 21 residues processed: 154 average time/residue: 0.0834 time to fit residues: 17.9682 Evaluate side-chains 146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.214034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.176242 restraints weight = 9227.844| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.68 r_work: 0.4213 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7567 Z= 0.174 Angle : 0.719 11.711 10225 Z= 0.362 Chirality : 0.046 0.162 1127 Planarity : 0.004 0.046 1286 Dihedral : 15.135 163.360 1171 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.65 % Allowed : 16.02 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.00 (0.29), residues: 908 helix: 1.79 (0.29), residues: 310 sheet: 0.43 (0.26), residues: 390 loop : -0.40 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.021 0.002 TYR A 115 PHE 0.024 0.002 PHE D 109 TRP 0.011 0.001 TRP D 94 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7565) covalent geometry : angle 0.71773 (10221) SS BOND : bond 0.00587 ( 2) SS BOND : angle 2.05457 ( 4) hydrogen bonds : bond 0.03141 ( 531) hydrogen bonds : angle 5.52118 ( 1530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.298 Fit side-chains REVERT: B 231 MET cc_start: 0.7279 (tpt) cc_final: 0.6943 (tpt) REVERT: B 247 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (t) outliers start: 36 outliers final: 27 residues processed: 147 average time/residue: 0.0687 time to fit residues: 14.4743 Evaluate side-chains 152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.215330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.177211 restraints weight = 9325.098| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.75 r_work: 0.4211 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7567 Z= 0.166 Angle : 0.730 12.819 10225 Z= 0.361 Chirality : 0.046 0.170 1127 Planarity : 0.004 0.047 1286 Dihedral : 14.877 163.116 1171 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.01 % Allowed : 17.31 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.04 (0.29), residues: 908 helix: 1.88 (0.29), residues: 310 sheet: 0.38 (0.27), residues: 386 loop : -0.32 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.020 0.002 TYR A 115 PHE 0.017 0.002 PHE C 109 TRP 0.012 0.001 TRP D 94 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7565) covalent geometry : angle 0.72936 (10221) SS BOND : bond 0.00166 ( 2) SS BOND : angle 2.00455 ( 4) hydrogen bonds : bond 0.03075 ( 531) hydrogen bonds : angle 5.50862 ( 1530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.375 Fit side-chains REVERT: C 115 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 247 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7612 (t) outliers start: 31 outliers final: 26 residues processed: 140 average time/residue: 0.0721 time to fit residues: 14.3425 Evaluate side-chains 146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.212791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.174817 restraints weight = 9144.916| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.68 r_work: 0.4193 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7567 Z= 0.199 Angle : 0.774 13.030 10225 Z= 0.384 Chirality : 0.046 0.176 1127 Planarity : 0.005 0.047 1286 Dihedral : 14.817 162.315 1171 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.88 % Allowed : 17.83 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.93 (0.29), residues: 908 helix: 1.89 (0.29), residues: 310 sheet: 0.29 (0.27), residues: 382 loop : -0.47 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.020 0.002 TYR B 115 PHE 0.017 0.002 PHE D 109 TRP 0.010 0.001 TRP D 94 HIS 0.005 0.002 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7565) covalent geometry : angle 0.77324 (10221) SS BOND : bond 0.00130 ( 2) SS BOND : angle 1.96284 ( 4) hydrogen bonds : bond 0.03212 ( 531) hydrogen bonds : angle 5.60104 ( 1530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.291 Fit side-chains REVERT: C 115 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 155 LYS cc_start: 0.7403 (mttp) cc_final: 0.6980 (mtpt) REVERT: A 342 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7308 (ttp) REVERT: D 115 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7436 (tm-30) outliers start: 30 outliers final: 27 residues processed: 135 average time/residue: 0.0735 time to fit residues: 13.9408 Evaluate side-chains 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.215601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.177574 restraints weight = 9094.529| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.71 r_work: 0.4217 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7567 Z= 0.163 Angle : 0.748 13.286 10225 Z= 0.370 Chirality : 0.046 0.161 1127 Planarity : 0.004 0.047 1286 Dihedral : 14.603 162.277 1171 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.49 % Allowed : 18.35 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.97 (0.29), residues: 908 helix: 1.97 (0.29), residues: 310 sheet: 0.26 (0.27), residues: 382 loop : -0.43 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.020 0.002 TYR B 115 PHE 0.029 0.002 PHE C 109 TRP 0.012 0.001 TRP D 94 HIS 0.005 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7565) covalent geometry : angle 0.74745 (10221) SS BOND : bond 0.00120 ( 2) SS BOND : angle 1.89212 ( 4) hydrogen bonds : bond 0.03065 ( 531) hydrogen bonds : angle 5.51861 ( 1530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.314 Fit side-chains REVERT: C 115 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 247 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7563 (t) REVERT: D 115 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7382 (tm-30) outliers start: 27 outliers final: 26 residues processed: 130 average time/residue: 0.0727 time to fit residues: 13.8314 Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 342 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.212038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.173981 restraints weight = 9202.522| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.69 r_work: 0.4185 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7567 Z= 0.209 Angle : 0.780 13.314 10225 Z= 0.387 Chirality : 0.047 0.172 1127 Planarity : 0.005 0.046 1286 Dihedral : 14.731 161.248 1171 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.13 % Allowed : 18.09 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 0.89 (0.29), residues: 908 helix: 1.92 (0.29), residues: 310 sheet: 0.19 (0.27), residues: 380 loop : -0.42 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 110 TYR 0.020 0.002 TYR B 115 PHE 0.029 0.002 PHE D 109 TRP 0.009 0.001 TRP C 94 HIS 0.005 0.002 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 7565) covalent geometry : angle 0.77953 (10221) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.92451 ( 4) hydrogen bonds : bond 0.03269 ( 531) hydrogen bonds : angle 5.63019 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.33 seconds wall clock time: 30 minutes 58.69 seconds (1858.69 seconds total)